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commit/galaxy-central: martenson: data libs API documentation
by commits-noreply＠bitbucket.org 22 Oct '14

22 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7c66e468c602/ Changeset: 7c66e468c602 User: martenson Date: 2014-10-22 18:08:57+00:00 Summary: data libs API documentation Affected #: 1 file diff -r 2fd74c3386c8934297d2b85249539a17353d8269 -r 7c66e468c6024b2e17a70ffadae0ad080b174c68 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -370,8 +370,8 @@ :param encoded_dataset_id: the encoded id of the dataset to change :type encoded_dataset_id: an encoded id string + :returns: dict containing information about the dataset :rtype: dictionary - :returns: dict containing information about the dataset """ undelete = util.string_as_bool( kwd.get( 'undelete', False ) ) try: @@ -400,16 +400,34 @@ @expose_api def load( self, trans, **kwd ): """ - Load dataset from the given source into the library. + load( self, trans, **kwd ): + * POST /api/libraries/datasets + Load dataset from the given source into the library. + Source can be: + user directory - root folder specified in galaxy.ini as "$user_library_import_dir" + example path: path/to/galaxy/$user_library_import_dir/user(a)example.com/{user can browse everything here} + the folder with the user login has to be created beforehand + (admin)import directory - root folder specified in galaxy ini as "$library_import_dir" + example path: path/to/galaxy/$library_import_dir/{admin can browse everything here} + (admin)any absolute or relative path - option allowed with "allow_library_path_paste" in galaxy.ini + + :param encoded_folder_id: the encoded id of the folder to import dataset(s) to + :type encoded_folder_id: an encoded id string + :param source: source the datasets should be loaded form + :type source: str + :param link_data: flag whether to link the dataset to data or copy it to Galaxy, defaults to copy + while linking is set to True all symlinks will be resolved _once_ + :type link_data: bool + :param preserve_dirs: flag whether to preserve the directory structure when importing dir + if False only datasets will be imported + :type preserve_dirs: bool + :param file_type: file type of the loaded datasets, defaults to 'auto' (autodetect) + :type file_type: str + :param dbkey: dbkey of the loaded genome, defaults to '?' (unknown) + :type dbkey: str - :param encoded_folder_id: the encoded id of the folder to import dataset to - :type encoded_folder_id: an encoded id string - :param source: source of the dataset to be loaded - :type source: str - :param link_data: flag whether to link the dataset to data or copy it to Galaxy - :type link_data: bool - :param preserve_dirs: flag whether to preserver directory structure when importing dir - :type preserve_dirs: bool + :returns: dict containing information about the created upload job + :rtype: dictionary """ kwd[ 'space_to_tab' ] = 'False' @@ -443,9 +461,7 @@ if user_base_dir is None: raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' ) full_dir = os.path.join( user_base_dir, user_login ) - # path_to_root_import_folder = None if not path.lower().startswith( full_dir.lower() ): - # path_to_root_import_folder = path path = os.path.join( full_dir, path ) if not os.path.exists( path ): raise exceptions.RequestParameterInvalidException( 'Given path does not exist on the host.' ) 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: martenson: data libs: hide share button, render first page by default, fix admin imports from import_dir, fix height of folder item row changing on hover
by commits-noreply＠bitbucket.org 22 Oct '14

22 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2fd74c3386c8/ Changeset: 2fd74c3386c8 User: martenson Date: 2014-10-22 17:39:39+00:00 Summary: data libs: hide share button, render first page by default, fix admin imports from import_dir, fix height of folder item row changing on hover Affected #: 12 files diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 client/galaxy/scripts/mvc/library/library-dataset-view.js --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -504,7 +504,7 @@ tmpl_array.push(' <% if (item.get("can_user_manage")) { %>'); tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); + // tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); tmpl_array.push(' <% } %>'); diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js @@ -97,7 +97,7 @@ var library_page_size = prompt( 'How many libraries per page do you want to see?', Galaxy.libraries.preferences.get( 'library_page_size' ) ); if ( ( library_page_size != null ) && ( library_page_size == parseInt( library_page_size ) ) ) { Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( library_page_size ) } ); - Galaxy.libraries.libraryListView.render(); + Galaxy.libraries.libraryListView.render( { show_page: 1 } ); } }, diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -414,7 +414,6 @@ kwd[ 'space_to_tab' ] = 'False' kwd[ 'to_posix_lines' ] = 'True' - kwd[ 'dbkey' ] = kwd.get( 'dbkey', '?' ) kwd[ 'file_type' ] = kwd.get( 'file_type', 'auto' ) kwd[' link_data_only' ] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files' @@ -436,9 +435,8 @@ raise exceptions.AdminRequiredException( 'Only admins can import from importdir.' ) if not trans.app.config.library_import_dir: raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow admins to import into library from importdir.' ) - user_base_dir = trans.app.config.library_import_dir - - + import_base_dir = trans.app.config.library_import_dir + path = os.path.join( import_base_dir, path ) if source in [ 'userdir_file', 'userdir_folder' ]: user_login = trans.user.email user_base_dir = trans.app.config.user_library_import_dir @@ -472,9 +470,11 @@ library_bunch = upload_common.handle_library_params( trans, {}, trans.security.encode_id( folder.id ) ) abspath_datasets = [] kwd[ 'filesystem_paths' ] = path + if source in [ 'importdir_folder' ]: + kwd[ 'filesystem_paths' ] = os.path.join( import_base_dir, path ) params = util.Params( kwd ) # user wants to import one file only - if source == "userdir_file": + if source in [ "userdir_file", "importdir_file" ]: file = os.path.abspath( path ) abspath_datasets.append( trans.webapp.controllers[ 'library_common' ].make_library_uploaded_dataset( trans, 'api', params, os.path.basename( file ), file, 'server_dir', library_bunch ) ) @@ -482,14 +482,14 @@ if source == "userdir_folder": uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( trans, 'api', params, library_bunch, 200, '' ) - uploaded_datasets = uploaded_datasets_bunch[0] + uploaded_datasets = uploaded_datasets_bunch[ 0 ] if uploaded_datasets is None: raise exceptions.ObjectNotFound( 'Given folder does not contain any datasets.' ) for ud in uploaded_datasets: ud.path = os.path.abspath( ud.path ) abspath_datasets.append( ud ) - # user wants to import from path (admins only) - if source == "admin_path": + # user wants to import from path + if source in [ "admin_path", "importdir_folder" ]: # validate the path is within root uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( trans, 'api', params, library_bunch, 200, '' ) diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -504,7 +504,7 @@ tmpl_array.push(' <% if (item.get("can_user_manage")) { %>'); tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); + // tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); tmpl_array.push(' <% } %>'); diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -168,11 +168,11 @@ this.$el.find('#first_folder_item').after(rowView.el); - $('.library-row').hover(function() { - $(this).find('.show_on_hover').show(); - }, function () { - $(this).find('.show_on_hover').hide(); - }); + // $('.library-row').hover(function() { + // $(this).find('.show_on_hover').show(); + // }, function () { + // $(this).find('.show_on_hover').hide(); + // }); }, /** diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/mvc/library/library-librarytoolbar-view.js @@ -97,7 +97,7 @@ var library_page_size = prompt( 'How many libraries per page do you want to see?', Galaxy.libraries.preferences.get( 'library_page_size' ) ); if ( ( library_page_size != null ) && ( library_page_size == parseInt( library_page_size ) ) ) { Galaxy.libraries.preferences.set( { 'library_page_size': parseInt( library_page_size ) } ); - Galaxy.libraries.libraryListView.render(); + Galaxy.libraries.libraryListView.render( { show_page: 1 } ); } }, diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sortColumnClicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sortColumnClicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll();this.checkEmptiness()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sortColumnClicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el)},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sortColumnClicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll();this.checkEmptiness()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/scripts/packed/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/packed/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-librarytoolbar-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"showLibraryModal","click #include_deleted_chk":"includeDeletedChecked","click #page_size_prompt":"showPageSizePrompt"},initialize:function(d){this.options=_.defaults(this.options||{},d);this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},renderPaginator:function(e){this.options=_.extend(this.options,e);var d=this.templatePaginator();this.$el.find("#library_paginator").html(d({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown}))},showLibraryModal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.createNewLibrary()},Close:function(){d.modal.hide()}}})},createNewLibrary:function(){var f=this.serializeNewLibrary();if(this.valdiateNewLibrary(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clearLibraryModal();Galaxy.libraries.libraryListView.render();b.success("Library created.")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured.")}}})}else{b.error("Library's name is missing.")}return false},showPageSizePrompt:function(){var d=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));if((d!=null)&&(d==parseInt(d))){Galaxy.libraries.preferences.set({library_page_size:parseInt(d)});Galaxy.libraries.libraryListView.render()}},clearLibraryModal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},valdiateNewLibrary:function(d){return d.name!==""},includeDeletedChecked:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <form class="form-inline" role="form">');tmpl_array.push(' <span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div class="checkbox" style="height: 20px;">');tmpl_array.push(" <label>");tmpl_array.push(' <input id="include_deleted_chk" type="checkbox"> include deleted </input>');tmpl_array.push(" </label>");tmpl_array.push(" </div>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>');tmpl_array.push(" <% } %>");tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="library_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </form>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of libraries on page" id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"showLibraryModal","click #include_deleted_chk":"includeDeletedChecked","click #page_size_prompt":"showPageSizePrompt"},initialize:function(d){this.options=_.defaults(this.options||{},d);this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},renderPaginator:function(e){this.options=_.extend(this.options,e);var d=this.templatePaginator();this.$el.find("#library_paginator").html(d({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown}))},showLibraryModal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.createNewLibrary()},Close:function(){d.modal.hide()}}})},createNewLibrary:function(){var f=this.serializeNewLibrary();if(this.valdiateNewLibrary(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clearLibraryModal();Galaxy.libraries.libraryListView.render();b.success("Library created.")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured.")}}})}else{b.error("Library's name is missing.")}return false},showPageSizePrompt:function(){var d=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));if((d!=null)&&(d==parseInt(d))){Galaxy.libraries.preferences.set({library_page_size:parseInt(d)});Galaxy.libraries.libraryListView.render({show_page:1})}},clearLibraryModal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},valdiateNewLibrary:function(d){return d.name!==""},includeDeletedChecked:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <form class="form-inline" role="form">');tmpl_array.push(' <span><strong><a href="#" title="Go to first page">DATA LIBRARIES</a></strong></span>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div class="checkbox" style="height: 20px;">');tmpl_array.push(" <label>");tmpl_array.push(' <input id="include_deleted_chk" type="checkbox"> include deleted </input>');tmpl_array.push(" </label>");tmpl_array.push(" </div>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>');tmpl_array.push(" <% } %>");tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="library_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </form>");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of libraries on page" id="page_size_prompt"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1322,6 +1322,7 @@ .ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none} .ui-select-multiple{height:100% !important;width:100% !important} .libraryRow{background-color:#ebd9b2} +tr{height:32px} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} div.libraryItemBody{padding:4px 4px 2px 4px} diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -1,6 +1,7 @@ a{text-decoration:underline} label{font-weight:normal} .libraryRow{background-color:#ebd9b2} +tr{height:32px} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} div.libraryItemBody{padding:4px 4px 2px 4px} diff -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 -r 2fd74c3386c8934297d2b85249539a17353d8269 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -5,6 +5,9 @@ background-color: @table-heading-bg; } +tr{ + height: 32px; +} .datasetHighlighted { background-color: @table-bg-accent; } 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

[galaxyproject/usegalaxy-playbook] c364a1: Update Main, update Main Pulsar, add nagios checks...
by GitHub 22 Oct '14

22 Oct '14

1 0

[galaxyproject/usegalaxy-playbook] 8d5aad: Get changed mutable configs on Test
by GitHub 22 Oct '14

22 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8d5aada303c061abe34e37fb7d1dd7d2928f7c4c https://github.com/galaxyproject/usegalaxy-playbook/commit/8d5aada303c061ab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-22 (Wed, 22 Oct 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Get changed mutable configs on Test

1 0

[galaxyproject/usegalaxy-playbook] c24a01: Update Test/Pulsar.
by GitHub 21 Oct '14

21 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c24a01d929076abe2155c36c45b6cfed040a5171 https://github.com/galaxyproject/usegalaxy-playbook/commit/c24a01d929076abe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-21 (Tue, 21 Oct 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M stage/group_vars/all.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Test/Pulsar.

1 0

commit/galaxy-central: jmchilton: Require pyyaml egg before using.
by commits-noreply＠bitbucket.org 21 Oct '14

21 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/28a24d7d3e84/ Changeset: 28a24d7d3e84 User: jmchilton Date: 2014-10-21 16:32:57+00:00 Summary: Require pyyaml egg before using. Thanks @natefoo. Affected #: 1 file diff -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 -r 28a24d7d3e84e5c9ce7af1dd92f7a89d83159703 lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -6,6 +6,8 @@ from galaxy.util.bunch import Bunch from galaxy import web +from galaxy import eggs +eggs.require("PyYAML") import yaml from galaxy.managers import api_keys 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: natefoo: Update tag latest_2014.10.06 for changeset a7b2aabb27ff
by commits-noreply＠bitbucket.org 21 Oct '14

21 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1e1beeb5322/ Changeset: d1e1beeb5322 Branch: stable User: natefoo Date: 2014-10-21 13:00:16+00:00 Summary: Update tag latest_2014.10.06 for changeset a7b2aabb27ff Affected #: 1 file diff -r a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 -r d1e1beeb532239250396dd8fbdc0156508c6744e .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -e1404e285ccb9e52bd09c5827934cd0da1974acc latest_2014.10.06 +a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 latest_2014.10.06 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: 161 new changesets
by commits-noreply＠bitbucket.org 20 Oct '14

20 Oct '14

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commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-ie (pull request #533)
by commits-noreply＠bitbucket.org 20 Oct '14

20 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/70f7ff8c6a96/ Changeset: 70f7ff8c6a96 User: jmchilton Date: 2014-10-20 21:22:27+00:00 Summary: Merged in jmchilton/galaxy-central-ie (pull request #533) Interactive Environments Plugin Framework with IPython Plugin Affected #: 35 files diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 client/galaxy/scripts/galaxy.interactive_environments.js --- /dev/null +++ b/client/galaxy/scripts/galaxy.interactive_environments.js @@ -0,0 +1,59 @@ +/** + * Internal function to remove content from the main area and add the notebook. + * Not idempotent + */ +function append_notebook(url){ + clear_main_area(); + $('#main').append('<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:hidden;" scrolling="no" src="'+ url +'"></iframe>' + ); +} + +function clear_main_area(){ + $('#spinner').remove(); + $('#main').children().remove(); +} + +function display_spinner(){ + $('#main').append('<img id="spinner" src="' + galaxy_root + '/static/style/largespinner.gif" style="position:absolute;margin:auto;top:0;left:0;right:0;bottom:0;">'); +} + + +/** + * Test availability of a URL, and call a callback when done. + * http://stackoverflow.com/q/25390206/347368 + * @param {String} url: URL to test availability of. Must return a 200 (302->200 is OK). + * @param {String} callback: function to call once successfully connected. + * + */ +function test_ie_availability(url, success_callback){ + var request_count = 0; + display_spinner(); + interval = setInterval(function(){ + $.ajax({ + url: url, + xhrFields: { + withCredentials: true + }, + type: "GET", + timeout: 500, + success: function(){ + console.log("Connected to IE, returning"); + clearInterval(interval); + success_callback(); + }, + error: function(jqxhr, status, error){ + request_count++; + console.log("Request " + request_count); + if(request_count > 30){ + clearInterval(interval); + clear_main_area(); + toastr.error( + "Could not connect to IE, contact your administrator", + "Error", + {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': false} + ); + } + } + }); + }, 1000); +} diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -249,6 +249,8 @@ <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/><datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/> + <datatype extension="ipynb" type="galaxy.datatypes.text:Ipynb" display_in_upload="True" /> + <datatype extension="json" type="galaxy.datatypes.text:Json" display_in_upload="True" /><datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/><datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/> @@ -292,6 +294,8 @@ <sniffer type="galaxy.datatypes.tabular:Sam"/><sniffer type="galaxy.datatypes.data:Newick"/><sniffer type="galaxy.datatypes.data:Nexus"/> + <sniffer type="galaxy.datatypes.text:Ipynb"/> + <sniffer type="galaxy.datatypes.text:Json"/><sniffer type="galaxy.datatypes.images:Jpg"/><sniffer type="galaxy.datatypes.images:Png"/><sniffer type="galaxy.datatypes.images:Tiff"/> diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -221,9 +221,15 @@ # Visualizations config directory: where to look for individual visualization plugins. # The path is relative to the Galaxy root dir. To use an absolute path begin the path -# with '/'. Defaults to "config/plugins/visualizations". +# with '/'. This is a comma separated list. Defaults to "config/plugins/visualizations". #visualization_plugins_directory = config/plugins/visualizations +# Interactive environment plugins root directory: where to look for interactive environment +# plugins. By default none will be loaded. Set to config/plugins/interactive_environments +# to load Galaxy's stock plugins (currently just IPython). These will require Docker +# to be configured and have security considerations so proceed with caution. +#interactive_environment_plugins_directory = + # Each job is given a unique empty directory as its current working directory. # This option defines in what parent directory those directories will be # created. @@ -421,6 +427,11 @@ # - $iso8601 (complete format string as specified by ISO 8601 international standard). # pretty_datetime_format = $locale (UTC) +# URL (with schema http/https) of the Galaxy instance as accessible within your local +# network - if specified used as a default by pulsar file staging and IPython docker +# container for communicating back with Galaxy via the API. +#galaxy_infrastructure_url = http://localhost:8080 + # The URL of the page to display in Galaxy's middle pane when loaded. This can be # an absolute or relative URL. #welcome_url = /static/welcome.html @@ -517,6 +528,26 @@ # requests. #nginx_upload_path = False +# Have Galaxy manage dynamic proxy component for routing requests to other +# services based on Galaxy's session cookie. It will attempt to do this by +# default though you do need to install node+npm and do an npm install from +# `lib/galaxy/web/proxy/js`. It is generally more robust to configure this +# externally managing it however Galaxy is managed. If True Galaxy will only +# launch the proxy if it is actually going to be used (e.g. for IPython). +#dynamic_proxy_manage=True + +# Dynamic proxy can use an SQLite database or a JSON file for IPC, set that +# here. +#dynamic_proxy_session_map=database/session_map.sqlite + +# Set the port and IP for the the dynamic proxy to bind to, this must match +# the external configuration if dynamic_proxy_manage is False. +#dynamic_proxy_bind_port=8800 +#dynamic_proxy_bind_ip=0.0.0.0 + +# Enable verbose debugging of Galaxy-managed dynamic proxy. +#dynamic_proxy_debug=False + # -- Logging and Debugging # Verbosity of console log messages. Acceptable values can be found here: @@ -549,6 +580,12 @@ # by setting the following option to True. #serve_xss_vulnerable_mimetypes = False +# Set the following to True to use ipython nbconvert to build HTML from IPython +# notebooks in Galaxy histories. This process may allow users to execute arbitrary +# code or serve arbitrary HTML. If enabled ipython must be available and on Galaxy's +# PATH, to do this run `pip install jinja2 pygments ipython` in Galaxy's virtualenv. +#trust_ipython_notebook_conversion = False + # Debug enables access to various config options useful for development and # debugging: use_lint, use_profile, use_printdebug and use_interactive. It # also causes the files used by PBS/SGE (submission script, output, and error) diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -50,7 +50,9 @@ <param id="amqp_url">amqp://guest:guest@localhost:5672//</param> + instance to/from. This can be unspecified/empty if + galaxy_infrastructure_url is set in galaxy.ini. + --><param id="galaxy_url">http://localhost:8080</param> diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/plugins/interactive_environments/common/templates/ie.mako --- /dev/null +++ b/config/plugins/interactive_environments/common/templates/ie.mako @@ -0,0 +1,31 @@ +<%def name="default_javascript_variables()"> +// Globals + +// Following three are for older-style IE proxies, newer dynamic Galaxy proxy +// does not use these. +ie_password_auth = ${ ie_request.javascript_boolean(ie_request.attr.PASSWORD_AUTH) }; +ie_apache_urls = ${ ie_request.javascript_boolean(ie_request.attr.APACHE_URLS) }; +ie_password = '${ ie_request.attr.notebook_pw }'; + + +var galaxy_root = '${ ie_request.attr.root }'; +var app_root = '${ ie_request.attr.app_root }'; +</%def> + + +<%def name="load_default_js()"> +${h.css( 'base' ) } +${h.js( 'libs/jquery/jquery', + 'libs/toastr', + 'libs/require')} +</%def> + +<%def name="plugin_require_config()"> +require.config({ + baseUrl: app_root, + paths: { + "plugin" : app_root + "js/", + "interactive_environments": "${h.url_for('/static/scripts/galaxy.interactive_environments')}", + }, +}); +</%def> diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/plugins/interactive_environments/interactive_environments.dtd --- /dev/null +++ b/config/plugins/interactive_environments/interactive_environments.dtd @@ -0,0 +1,1 @@ +../visualizations/visualization.dtd \ No newline at end of file diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/plugins/interactive_environments/ipython/config/ipython.ini.sample --- /dev/null +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -0,0 +1,16 @@ +[main] + +# Following options are ignored if using the Galaxy dynamic proxy but +# are useful if mapping a range of ports for environment consumption. +#apache_urls = False +#password_auth = False +#ssl = False + +[docker] +command = docker +image = bgruening/docker-ipython-notebook + +# URL to access the Galaxy API with from the spawn Docker containter, if empty +# this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the +# Docker host of the spawned container if that is also not set. +#galaxy_url = diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/plugins/interactive_environments/ipython/config/ipython.xml --- /dev/null +++ b/config/plugins/interactive_environments/ipython/config/ipython.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd"> +<interactive_environment name="IPython"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Text</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + </params> + <template>ipython.mako</template> +</interactive_environment> diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/plugins/interactive_environments/ipython/static/js/ipython.js --- /dev/null +++ b/config/plugins/interactive_environments/ipython/static/js/ipython.js @@ -0,0 +1,85 @@ +function message_failed_auth(password){ + toastr.info( + "Automatic authorization failed. You can manually login with:<br>" + password + "<br><a href='https://github.com/bgruening/galaxy-ipython/wiki/Automatic-Authorization-Fa…' target='_blank'>More details ...</a>", + "Please login manually", + {'closeButton': true, 'timeOut': 100000, 'tapToDismiss': false} + ); +} + +function message_failed_connection(){ + toastr.error( + "Could not connect to IPython Notebook. Please contact your administrator. <a href='https://github.com/bgruening/galaxy-ipython/wiki/Could-not-connect-to-IPyth…' target='_blank'>More details ...</a>", + "Security warning", + {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': true} + ); +} + +function message_no_auth(){ + // No longer a security issue, proxy validates Galaxy session token. + /* + toastr.warning( + "IPython Notebook was lunched without authentication. This is a security issue. <a href='https://github.com/bgruening/galaxy-ipython/wiki/IPython-Notebook-was-lunch…' target='_blank'>More details ...</a>", + "Security warning", + {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': false} + ); + */ +} + + +/** + * Load an interactive environment (IE) from a remote URL + * @param {String} password: password used to authenticate to the remote resource + * @param {String} notebook_login_url: URL that should be POSTed to for login + * @param {String} notebook_access_url: the URL embeded in the page and loaded + * + */ +function load_notebook(password, notebook_login_url, notebook_access_url){ + $( document ).ready(function() { + // Test notebook_login_url for accessibility, executing the login+load function whenever + // we've successfully connected to the IE. + test_ie_availability(notebook_login_url, function(){ + _handle_notebook_loading(password, notebook_login_url, notebook_access_url); + }); + }); +} + +/** + * Must be implemented by IEs + */ +function _handle_notebook_loading(password, notebook_login_url, notebook_access_url){ + if ( ie_password_auth ) { + // Make an AJAX POST + $.ajax({ + type: "POST", + // to the Login URL + url: notebook_login_url, + // With our password + data: { + 'password': password + }, + xhrFields: { + withCredentials: true + }, + // If that is successful, load the notebook + success: function(){ + append_notebook(notebook_access_url); + }, + error: function(jqxhr, status, error){ + if(ie_password_auth && !ie_apache_urls){ + // Failure happens due to CORS + message_failed_auth(password); + append_notebook(notebook_access_url); + }else{ + message_failed_connection(); + // Do we want to try and load the notebook anyway? Just in case? + append_notebook(notebook_access_url); + } + } + }); + } + else { + // Not using password auth, just embed it to avoid content-origin issues. + message_no_auth(); + append_notebook(notebook_access_url); + } +} diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/plugins/interactive_environments/ipython/templates/ipython.mako --- /dev/null +++ b/config/plugins/interactive_environments/ipython/templates/ipython.mako @@ -0,0 +1,61 @@ + <%namespace name="ie" file="ie.mako" /> + +<% +import os +import shutil +import tempfile +import subprocess + +# Sets ID and sets up a lot of other variables +ie_request.load_deploy_config() +ie_request.attr.docker_port = 6789 +# Create tempdir in galaxy +temp_dir = os.path.abspath( tempfile.mkdtemp() ) +# Write out conf file...needs work +ie_request.write_conf_file(temp_dir) + +## IPython Specific +# Prepare an empty notebook +notebook_id = ie_request.generate_hex(64) +with open( os.path.join( ie_request.attr.our_template_dir, 'notebook.ipynb' ), 'r') as nb_handle: + empty_nb = nb_handle.read() +empty_nb = empty_nb % notebook_id +# Copy over default notebook, unless the dataset this viz is running on is a notebook +empty_nb_path = os.path.join(temp_dir, 'ipython_galaxy_notebook.ipynb') +if hda.datatype.__class__.__name__ != "Ipynb": + with open( empty_nb_path, 'w+' ) as handle: + handle.write( empty_nb ) +else: + shutil.copy( hda.file_name, empty_nb_path ) + + +## General IE specific +# Access URLs for the notebook from within galaxy. +notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/notebooks/ipython_galaxy_notebook.ipynb') +notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/login?next=%2Fipython%2F${PORT}%2Ftree') + +docker_cmd = ie_request.docker_cmd(temp_dir) +subprocess.call(docker_cmd, shell=True) +%> +<html> +<head> +${ ie.load_default_js() } +</head> +<body> + +<script type="text/javascript"> +${ ie.default_javascript_variables() } +var notebook_login_url = '${ notebook_login_url }'; +var notebook_access_url = '${ notebook_access_url }'; +${ ie.plugin_require_config() } + +// Load notebook + +requirejs(['interactive_environments', 'plugin/ipython'], function(){ + load_notebook(ie_password, notebook_login_url, notebook_access_url); +}); +</script> +<div id="main" width="100%" height="100%"> +</div> +</body> +</html> diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/plugins/interactive_environments/ipython/templates/notebook.ipynb --- /dev/null +++ b/config/plugins/interactive_environments/ipython/templates/notebook.ipynb @@ -0,0 +1,43 @@ +{ + "metadata": { + "name": "", + "signature": "sha256:%s" + }, + "nbformat": 3, + "nbformat_minor": 0, + "worksheets": [ + { + "cells": [ + { + "cell_type": "heading", + "level": 1, + "metadata": {}, + "source": [ + "Welcome to the interactive Galaxy IPython Notebook." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You can access your data via the dataset number. For example, ``handle = get(42)``.", + "To save data, write your data to a file, and then call ``put('filename.txt')``. The dataset will then be available in your galaxy history.", + "Notebooks can be saved to Galaxy by clicking the large green button at the top right of the IPython interface.<br>", + "More help and informations can be found on the project [website](https://github.com/bgruening/galaxy-ipython)." + ] + }, + { + "cell_type": "code", + "collapsed": false, + "input": [ + ], + "language": "python", + "metadata": {}, + "outputs": [], + "prompt_number": 1 + } + ], + "metadata": {} + } + ] +} diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/plugins/visualizations/additional_template_paths.xml --- a/config/plugins/visualizations/additional_template_paths.xml +++ b/config/plugins/visualizations/additional_template_paths.xml @@ -2,4 +2,5 @@ <paths><path>common/templates</path> + <path>../interactive_environments/common/templates</path></paths> diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 config/plugins/visualizations/visualization.dtd --- a/config/plugins/visualizations/visualization.dtd +++ b/config/plugins/visualizations/visualization.dtd @@ -1,5 +1,6 @@ <!ELEMENT visualization (description*,data_sources*,params*,template_root*,template,render_target*)> +<!ELEMENT interactive_environment (description*,data_sources*,params*,template_root*,template,render_target*)><!-- visualization name: the title/display name of the visualization (e.g. 'Trackster', 'Fastq Stats', etc.) REQUIRED disabled: if included (value does not matter), this attribute will prevent the visualization being loaded diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -17,6 +17,7 @@ from galaxy.tools.data_manager.manager import DataManagers from galaxy.jobs import metrics as job_metrics from galaxy.web.base import pluginframework +from galaxy.web.proxy import ProxyManager from galaxy.queue_worker import GalaxyQueueWorker from tool_shed.galaxy_install import update_repository_manager @@ -138,6 +139,7 @@ # FIXME: These are exposed directly for backward compatibility self.job_queue = self.job_manager.job_queue self.job_stop_queue = self.job_manager.job_stop_queue + self.proxy_manager = ProxyManager( self.config ) # Initialize the external service types self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self ) self.model.engine.dispose() diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -18,6 +18,8 @@ from galaxy.util.dbkeys import GenomeBuilds from galaxy import eggs +import ConfigParser + log = logging.getLogger( __name__ ) @@ -208,6 +210,7 @@ self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) + self.trust_ipython_notebook_conversion = string_as_bool( kwargs.get( 'trust_ipython_notebook_conversion', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) self.brand = kwargs.get( 'brand', None ) self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) @@ -296,6 +299,23 @@ for section in global_conf_parser.sections(): if section.startswith('server:'): self.server_names.append(section.replace('server:', '', 1)) + + # Default URL (with schema http/https) of the Galaxy instance within the + # local network - used to remotely communicate with the Galaxy API. + galaxy_infrastructure_url = kwargs.get( 'galaxy_infrastructure_url', None ) + galaxy_infrastructure_url_set = True + if galaxy_infrastructure_url is None: + # Still provide a default but indicate it was not explicitly set + # so dependending on the context a better default can be used ( + # request url in a web thread, Docker parent in IE stuff, etc...) + galaxy_infrastructure_url = "http://localhost" + port = self.guess_galaxy_port() + if port: + galaxy_infrastructure_url += ":%s" % (port) + galaxy_infrastructure_url_set = False + self.galaxy_infrastructure_url = galaxy_infrastructure_url + self.galaxy_infrastructure_url_set = galaxy_infrastructure_url_set + # Store advanced job management config self.job_manager = kwargs.get('job_manager', self.server_name).strip() self.job_handlers = [ x.strip() for x in kwargs.get('job_handlers', self.server_name).split(',') ] @@ -357,6 +377,18 @@ # directory where the visualization/registry searches for plugins self.visualization_plugins_directory = kwargs.get( 'visualization_plugins_directory', 'config/plugins/visualizations' ) + ie_dirs = kwargs.get( 'interactive_environment_plugins_directory', None ) + if ie_dirs and not self.visualization_plugins_directory: + self.visualization_plugins_directory = ie_dirs + elif ie_dirs: + self.visualization_plugins_directory += ",%s" % ie_dirs + + self.proxy_session_map = self.resolve_path( kwargs.get( "dynamic_proxy_session_map", "database/session_map.sqlite" ) ) + self.manage_dynamic_proxy = string_as_bool( kwargs.get( "dynamic_proxy_manage", "True" ) ) # Set to false if being launched externally + self.dynamic_proxy_debug = string_as_bool( kwargs.get( "dynamic_proxy_debug", "False" ) ) + self.dynamic_proxy_bind_port = int( kwargs.get( "dynamic_proxy_bind_port", "8800" ) ) + self.dynamic_proxy_bind_ip = kwargs.get( "dynamic_proxy_bind_ip", "0.0.0.0" ) + # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) @@ -543,6 +575,19 @@ """ return resolve_path( path, self.root ) + def guess_galaxy_port(self): + # Code derived from IPython work ie.mako + config = ConfigParser.SafeConfigParser({'port': '8080'}) + if self.config_file: + config.read( self.config_file ) + + try: + port = config.getint('server:%s' % self.server_name, 'port') + except: + # uWSGI galaxy installations don't use paster and only speak uWSGI not http + port = None + return port + def get_database_engine_options( kwargs, model_prefix='' ): """ diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -22,6 +22,7 @@ import assembly import ngsindex import graph +import text import galaxy.util from galaxy.util.odict import odict from display_applications.application import DisplayApplication diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/datatypes/text.py --- /dev/null +++ b/lib/galaxy/datatypes/text.py @@ -0,0 +1,121 @@ +# -*- coding: utf-8 -*- +""" Clearing house for generic text datatypes that are not XML or tabular. +""" + + +from galaxy.datatypes.data import Text +from galaxy.datatypes.data import get_file_peek +from galaxy.datatypes.data import nice_size +from galaxy import util + +import tempfile +import subprocess +import json +import os + +import logging +log = logging.getLogger(__name__) + + +class Json( Text ): + file_ext = "json" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = "JavaScript Object Notation (JSON)" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disc' + + def sniff( self, filename ): + """ + Try to load the string with the json module. If successful it's a json file. + """ + return self._looks_like_json( filename ) + + def _looks_like_json( self, filename ): + # Pattern used by SequenceSplitLocations + if os.path.getsize(filename) < 50000: + # If the file is small enough - don't guess just check. + try: + json.load( open(filename, "r") ) + return True + except Exception: + return False + else: + with open(filename, "r") as fh: + while True: + line = fh.readline() + line = line.strip() + if line: + # simple types are valid JSON as well - but would such a file + # be interesting as JSON in Galaxy? + return line.startswith("[") or line.startswith("{") + return False + + def display_peek( self, dataset ): + try: + return dataset.peek + except: + return "JSON file (%s)" % ( nice_size( dataset.get_size() ) ) + + +class Ipynb( Json ): + file_ext = "ipynb" + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = "IPython Notebook" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disc' + + def sniff( self, filename ): + """ + Try to load the string with the json module. If successful it's a json file. + """ + if self._looks_like_json( filename ): + try: + ipynb = json.load( open(filename) ) + if ipynb.get('nbformat', False) is not False and ipynb.get('metadata', False): + return True + else: + return False + except: + return False + + def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd): + config = trans.app.config + trust = getattr( config, 'trust_ipython_notebook_conversion', False ) + if trust: + return self._display_data_trusted(trans, dataset, preview=preview, fileame=filename, to_ext=to_ext, chunk=chunk, **kwd) + else: + return super(Ipynb, self).display_data( trans, dataset, preview=preview, fileame=filename, to_ext=to_ext, chunk=chunk, **kwd ) + + def _display_data_trusted(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd): + preview = util.string_as_bool( preview ) + if chunk: + return self.get_chunk(trans, dataset, chunk) + elif to_ext or not preview: + return self._serve_raw(trans, dataset, to_ext) + else: + ofile_handle = tempfile.NamedTemporaryFile(delete=False) + ofilename = ofile_handle.name + ofile_handle.close() + try: + cmd = 'ipython nbconvert --to html --template basic %s --output %s' % (dataset.file_name, ofilename) + log.info("Calling command %s" % cmd) + subprocess.call(cmd, shell=True) + ofilename = '%s.html' % ofilename + except: + ofilename = dataset.file_name + log.exception( 'Command "%s" failed. Could not convert the IPython Notebook to HTML, defaulting to plain text.' % cmd ) + return open( ofilename ) + + def set_meta( self, dataset, **kwd ): + """ + Set the number of models in dataset. + """ + pass diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/jobs/runners/pulsar.py --- a/lib/galaxy/jobs/runners/pulsar.py +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -53,7 +53,7 @@ ), galaxy_url=dict( map=specs.to_str_or_none, - default=DEFAULT_GALAXY_URL, + default=None, ), manager=dict( map=specs.to_str_or_none, @@ -129,6 +129,8 @@ super( PulsarJobRunner, self ).__init__( app, nworkers, runner_param_specs=PULSAR_PARAM_SPECS, **kwds ) self._init_worker_threads() galaxy_url = self.runner_params.galaxy_url + if not galaxy_url: + galaxy_url = app.config.galaxy_infrastructure_url if galaxy_url: galaxy_url = galaxy_url.rstrip("/") self.galaxy_url = galaxy_url diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/util/lazy_process.py --- /dev/null +++ b/lib/galaxy/util/lazy_process.py @@ -0,0 +1,57 @@ +import threading +import time +import subprocess + + +class LazyProcess( object ): + """ Abstraction describing a command line launching a service - probably + as needed as functionality is accessed in Galaxy. + """ + + def __init__( self, command_and_args ): + self.command_and_args = command_and_args + self.thread_lock = threading.Lock() + self.allow_process_request = True + self.process = None + + def start_process( self ): + with self.thread_lock: + if self.allow_process_request: + self.allow_process_request = False + t = threading.Thread(target=self.__start) + t.daemon = True + t.start() + + def __start(self): + with self.thread_lock: + self.process = subprocess.Popen( self.command_and_args, close_fds=True ) + + def shutdown( self ): + with self.thread_lock: + self.allow_process_request = False + if self.running: + self.process.terminate() + time.sleep(.01) + if self.running: + self.process.kill() + + @property + def running( self ): + return self.process and not self.process.poll() + + +class NoOpLazyProcess( object ): + """ LazyProcess abstraction meant to describe potentially optional + services, in those cases where one is not configured or valid, this + class can be used in place of LazyProcess. + """ + + def start_process( self ): + return + + def shutdown( self ): + return + + @property + def running( self ): + return False diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/util/sockets.py --- /dev/null +++ b/lib/galaxy/util/sockets.py @@ -0,0 +1,43 @@ +import shlex +import socket +import subprocess +import random + + +def unused_port(range=None): + if range: + return __unused_port_on_range(range) + else: + return __unused_port_rangeless() + + +def __unused_port_rangeless(): + # TODO: Allow ranges (though then need to guess and check)... + s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) + s.bind(('localhost', 0)) + addr, port = s.getsockname() + s.close() + return port + + +def __unused_port_on_range(range): + assert range[0] and range[1] + + # Find all ports that are already occupied + cmd_netstat = shlex.split("netstat tuln") + p1 = subprocess.Popen(cmd_netstat, stdout=subprocess.PIPE) + + occupied_ports = set() + for line in p1.stdout.read().split('\n'): + if line.startswith('tcp') or line.startswith('tcp6'): + col = line.split() + local_address = col[3] + local_port = local_address.split(':')[1] + occupied_ports.add( int(local_port) ) + + # Generate random free port number. + while True: + port = random.randrange(range[0], range[1]) + if port not in occupied_ports: + break + return port diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -344,6 +344,10 @@ # TODO: As part of a future note plugin registry effort - move this # override and let VisualizationsRegistry just revert to using parent's # fill_template. + + # No longer needed but being left around for a few releases as ipython-galaxy + # as an external visualization plugin is deprecated in favor of core interactive + # environment plugin. if 'get_api_key' not in kwargs: def get_api_key(): @@ -401,6 +405,10 @@ """ returned = {} + # main tag specifies plugin type (visualization or + # interactive_enviornment). + returned[ 'plugin_type' ] = xml_tree.tag + # a text display name for end user links returned[ 'name' ] = xml_tree.attrib.get( 'name', None ) if not returned[ 'name' ]: diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/base/interactive_environments.py --- /dev/null +++ b/lib/galaxy/web/base/interactive_environments.py @@ -0,0 +1,162 @@ +import ConfigParser + +import hashlib +import os +import random + +from galaxy.util.bunch import Bunch +from galaxy import web +import yaml +from galaxy.managers import api_keys + + +class InteractiveEnviornmentRequest(object): + + def __init__(self, trans, plugin): + plugin_config = plugin.config + + self.trans = trans + + self.attr = Bunch() + self.attr.viz_id = plugin_config["name"].lower() + self.attr.history_id = trans.security.encode_id( trans.history.id ) + self.attr.proxy_request = trans.app.proxy_manager.setup_proxy( trans ) + self.attr.proxy_url = self.attr.proxy_request[ 'proxy_url' ] + self.attr.galaxy_config = trans.app.config + self.attr.galaxy_root_dir = os.path.abspath(self.attr.galaxy_config.root) + + self.attr.root = web.url_for("/") + self.attr.app_root = self.attr.root + "plugins/visualizations/" + self.attr.viz_id + "/static/" + + plugin_path = os.path.abspath( plugin.path ) + + # Store our template and configuration path + self.attr.our_config_dir = os.path.join(plugin_path, "config") + self.attr.our_template_dir = os.path.join(plugin_path, "templates") + self.attr.HOST = trans.request.host.rsplit(':', 1)[0] + self.attr.PORT = self.attr.proxy_request[ 'proxied_port' ] + + def load_deploy_config(self, default_dict={}): + viz_config = ConfigParser.SafeConfigParser(default_dict) + conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" ) + if not os.path.exists( conf_path ): + conf_path = "%s.sample" % conf_path + viz_config.read( conf_path ) + self.attr.viz_config = viz_config + + def _boolean_option(option, default=False): + if self.attr.viz_config.has_option("main", option): + return self.attr.viz_config.getboolean("main", option) + else: + return default + + # Older style port range proxying - not sure we want to keep these around or should + # we always assume use of Galaxy dynamic proxy? None of these need to be specified + # if using the Galaxy dynamic proxy. + self.attr.PASSWORD_AUTH = _boolean_option("password_auth") + self.attr.APACHE_URLS = _boolean_option("apache_urls") + self.attr.SSL_URLS = _boolean_option("ssl") + + def write_conf_file(self, output_directory, extra={}): + """ + Build up a configuration file that is standard for ALL IEs. + + TODO: replace hashed password with plaintext. + """ + trans = self.trans + request = trans.request + api_key = api_keys.ApiKeyManager( trans.app ).get_or_create_api_key( trans.user ) + conf_file = { + 'history_id': self.attr.history_id, + 'api_key': api_key, + 'remote_host': request.remote_addr, + 'docker_port': self.attr.PORT, + 'cors_origin': request.host_url, + } + + if self.attr.viz_config.has_option("docker", "galaxy_url"): + conf_file['galaxy_url'] = self.attr.viz_config.getstring("docker", "galaxy_url") + elif self.attr.galaxy_config.galaxy_infrastructure_url_set: + conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/' + else: + conf_file['galaxy_url'] = request.application_url.rstrip('/') + '/' + conf_file['galaxy_paster_port'] = self.attr.galaxy_config.guess_galaxy_port() + + if self.attr.PASSWORD_AUTH: + # Generate a random password + salt + notebook_pw_salt = self.generate_password(length=12) + notebook_pw = self.generate_password(length=24) + m = hashlib.sha1() + m.update( notebook_pw + notebook_pw_salt ) + conf_file['notebook_password'] = 'sha1:%s:%s' % (notebook_pw_salt, m.hexdigest()) + # Should we use password based connection or "default" connection style in galaxy + else: + notebook_pw = "None" + + # Some will need to pass extra data + for extra_key in extra: + conf_file[extra_key] = extra[extra_key] + + self.attr.notebook_pw = notebook_pw + # Write conf + with open( os.path.join( output_directory, 'conf.yaml' ), 'wb' ) as handle: + handle.write( yaml.dump(conf_file, default_flow_style=False) ) + + def generate_hex(self, length): + return ''.join(random.choice('0123456789abcdef') for _ in range(length)) + + def generate_password(self, length): + """ + Generate a random alphanumeric password + """ + return ''.join(random.choice('0123456789abcdefghijklmnopqrstuvwxyz') for _ in range(length)) + + def javascript_boolean(self, python_boolean): + """ + Convenience function to convert boolean for use in JS + """ + if python_boolean: + return "true" + else: + return "false" + + def url_template(self, url_template): + """ + Process a URL template + + There are several variables accessible to the user: + + - ${PROXY_URL} will be replaced with dynamically create proxy + - ${PORT} will be replaced with the port the docker image is attached to + """ + # Figure out our substitutions + + # Next several lines for older style replacements (not used with Galaxy dynamic + # proxy) + + if self.attr.SSL_URLS: + protocol = 'https' + else: + protocol = 'http' + + if not self.attr.APACHE_URLS: + # If they are not using apache URLs, that implies there's a port attached to the host + # string, thus we replace just the first instance of host that we see. + url_template = url_template.replace('${HOST}', '${HOST}:${PORT}', 1) + + url_template = url_template.replace('${PROTO}', protocol) \ + .replace('${HOST}', self.attr.HOST) + + # Only the following replacements are used with Galaxy dynamic proxy + # URLs + url = url_template.replace('${PROXY_URL}', str(self.attr.proxy_url)) \ + .replace('${PORT}', str(self.attr.PORT)) + return url + + def docker_cmd(self, temp_dir): + """ + Generate and return the docker command to execute + """ + return '%s run -d --sig-proxy=true -p %s:%s -v "%s:/import/" %s' % \ + (self.attr.viz_config.get("docker", "command"), self.attr.PORT, self.attr.docker_port, + temp_dir, self.attr.viz_config.get("docker", "image")) diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -20,6 +20,8 @@ from galaxy import util from galaxy.util import odict from galaxy.util import bunch +from .interactive_environments import InteractiveEnviornmentRequest + import logging log = logging.getLogger( __name__ ) @@ -590,6 +592,11 @@ if 'plugin_path' not in kwargs: kwargs[ 'plugin_path'] = os.path.abspath( plugin.path ) + plugin_type = plugin.config["plugin_type"] + if plugin_type == "interactive_environment": + request = InteractiveEnviornmentRequest(trans, plugin) + kwargs["ie_request"] = request + # defined here to be overridden return trans.fill_template( template_filename, template_lookup=plugin.template_lookup, **kwargs ) diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/proxy/__init__.py --- /dev/null +++ b/lib/galaxy/web/proxy/__init__.py @@ -0,0 +1,169 @@ +import logging +import os +import json + +from .filelock import FileLock +from galaxy.util import sockets +from galaxy.util.lazy_process import LazyProcess, NoOpLazyProcess +from galaxy.util import sqlite + +log = logging.getLogger( __name__ ) + + +DEFAULT_PROXY_TO_HOST = "localhost" +SECURE_COOKIE = "galaxysession" + + +class ProxyManager(object): + + def __init__( self, config ): + for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug" ]: + setattr( self, option, getattr( config, option ) ) + self.launch_by = "node" # TODO: Support docker + if self.manage_dynamic_proxy: + self.lazy_process = self.__setup_lazy_process( config ) + else: + self.lazy_process = NoOpLazyProcess() + self.proxy_ipc = proxy_ipc(config) + + def shutdown( self ): + self.lazy_process.shutdown() + + def setup_proxy( self, trans, host=DEFAULT_PROXY_TO_HOST, port=None ): + if self.manage_dynamic_proxy: + log.info("Attempting to start dynamic proxy process") + self.lazy_process.start_process() + + authentication = AuthenticationToken(trans) + proxy_requests = ProxyRequests(host=host, port=port) + self.proxy_ipc.handle_requests(authentication, proxy_requests) + # TODO: These shouldn't need to be request.host and request.scheme - + # though they are reasonable defaults. + host = trans.request.host + if ':' in host: + host = host[0:host.index(':')] + scheme = trans.request.scheme + proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port) + return { + 'proxy_url': proxy_url, + 'proxied_port': proxy_requests.port, + 'proxied_host': proxy_requests.host, + } + + def __setup_lazy_process( self, config ): + launcher = proxy_launcher(self) + command = launcher.launch_proxy_command(config) + return LazyProcess(command) + + +def proxy_launcher(config): + return NodeProxyLauncher() + + +class ProxyLauncher(object): + + def launch_proxy_command(self, config): + raise NotImplementedError() + + +class NodeProxyLauncher(object): + + def launch_proxy_command(self, config): + args = [ + "--sessions", config.proxy_session_map, + "--ip", config.dynamic_proxy_bind_ip, + "--port", str(config.dynamic_proxy_bind_port), + ] + if config.dynamic_proxy_debug: + args.append("--verbose") + + parent_directory = os.path.dirname( __file__ ) + path_to_application = os.path.join( parent_directory, "js", "lib", "main.js" ) + command = [ path_to_application ] + args + return command + + +class AuthenticationToken(object): + + def __init__(self, trans): + self.cookie_name = SECURE_COOKIE + self.cookie_value = trans.get_cookie( self.cookie_name ) + + +class ProxyRequests(object): + + def __init__(self, host=None, port=None): + if host is None: + host = DEFAULT_PROXY_TO_HOST + if port is None: + port = sockets.unused_port() + log.info("Obtained unused port %d" % port) + self.host = host + self.port = port + + +def proxy_ipc(config): + proxy_session_map = config.proxy_session_map + if proxy_session_map.endswith(".sqlite"): + return SqliteProxyIpc(proxy_session_map) + else: + return JsonFileProxyIpc(proxy_session_map) + + +class ProxyIpc(object): + + def handle_requests(self, cookie, host, port): + raise NotImplementedError() + + +class JsonFileProxyIpc(object): + + def __init__(self, proxy_session_map): + self.proxy_session_map = proxy_session_map + + def handle_requests(self, authentication, proxy_requests): + key = "%s:%s" % ( proxy_requests.host, proxy_requests.port ) + secure_id = authentication.cookie_value + with FileLock( self.proxy_session_map ): + if not os.path.exists( self.proxy_session_map ): + open( self.proxy_session_map, "w" ).write( "{}" ) + json_data = open( self.proxy_session_map, "r" ).read() + session_map = json.loads( json_data ) + to_remove = [] + for k, value in session_map.items(): + if value == secure_id: + to_remove.append( k ) + for k in to_remove: + del session_map[ k ] + session_map[ key ] = secure_id + new_json_data = json.dumps( session_map ) + open( self.proxy_session_map, "w" ).write( new_json_data ) + + +class SqliteProxyIpc(object): + + def __init__(self, proxy_session_map): + self.proxy_session_map = proxy_session_map + + def handle_requests(self, authentication, proxy_requests): + key = "%s:%s" % ( proxy_requests.host, proxy_requests.port ) + secure_id = authentication.cookie_value + with FileLock( self.proxy_session_map ): + conn = sqlite.connect(self.proxy_session_map) + try: + c = conn.cursor() + try: + # Create table + c.execute('''CREATE TABLE gxproxy + (key text PRIMARY_KEY, secret text)''') + except Exception: + pass + insert_tmpl = '''INSERT INTO gxproxy (key, secret) VALUES ('%s', '%s');''' + insert = insert_tmpl % (key, secure_id) + c.execute(insert) + conn.commit() + finally: + conn.close() + +# TODO: RESTful API driven proxy? +# TODO: MQ diven proxy? diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/proxy/filelock.py --- /dev/null +++ b/lib/galaxy/web/proxy/filelock.py @@ -0,0 +1,82 @@ +""" Code obtained from https://github.com/dmfrey/FileLock + +See full license at: + +https://github.com/dmfrey/FileLock/blob/master/LICENSE.txt + +""" +import os +import time +import errno + + +class FileLockException(Exception): + pass + + +class FileLock(object): + """ A file locking mechanism that has context-manager support so + you can use it in a with statement. This should be relatively cross + compatible as it doesn't rely on msvcrt or fcntl for the locking. + """ + + def __init__(self, file_name, timeout=10, delay=.05): + """ Prepare the file locker. Specify the file to lock and optionally + the maximum timeout and the delay between each attempt to lock. + """ + self.is_locked = False + full_path = os.path.abspath(file_name) + self.lockfile = "%s.lock" % full_path + self.file_name = full_path + self.timeout = timeout + self.delay = delay + + def acquire(self): + """ Acquire the lock, if possible. If the lock is in use, it check again + every `wait` seconds. It does this until it either gets the lock or + exceeds `timeout` number of seconds, in which case it throws + an exception. + """ + start_time = time.time() + while True: + try: + self.fd = os.open(self.lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR) + break + except OSError as e: + if e.errno != errno.EEXIST: + raise + if (time.time() - start_time) >= self.timeout: + raise FileLockException("Timeout occured.") + time.sleep(self.delay) + self.is_locked = True + + def release(self): + """ Get rid of the lock by deleting the lockfile. + When working in a `with` statement, this gets automatically + called at the end. + """ + if self.is_locked: + os.close(self.fd) + os.unlink(self.lockfile) + self.is_locked = False + + def __enter__(self): + """ Activated when used in the with statement. + Should automatically acquire a lock to be used in the with block. + """ + if not self.is_locked: + self.acquire() + return self + + def __exit__(self, type, value, traceback): + """ Activated at the end of the with statement. + It automatically releases the lock if it isn't locked. + """ + if self.is_locked: + self.release() + + def __del__(self): + """ Make sure that the FileLock instance doesn't leave a lockfile + lying around. + """ + self.release() diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/proxy/js/Dockerfile --- /dev/null +++ b/lib/galaxy/web/proxy/js/Dockerfile @@ -0,0 +1,18 @@ +# Have not yet gotten this to work - goal was to launch the prox in a Docker container. +# Networking is a bit tricky though - could not get the child proxy to talk to the child +# IPython container. + + +# sudo docker build --no-cache=true -t gxproxy . +# sudo docker run --net host -v /home/john/workspace/galaxy-central/database:/var/gxproxy -p 8800:8800 -t gxproxy lib/main.js --sessions /var/gxproxy/session_map.json --ip 0.0.0.0 --port 8800 + +FROM node:0.11.13 + +RUN mkdir -p /usr/src/gxproxy +WORKDIR /usr/src/gxproxy + +ADD package.json /usr/src/gxproxy/ +RUN npm install +ADD . /usr/src/gxproxy + +CMD [ "lib/main.js" ] diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/proxy/js/README.md --- /dev/null +++ b/lib/galaxy/web/proxy/js/README.md @@ -0,0 +1,2 @@ +# A dynamic configurable reverse proxy for use within Galaxy + diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/proxy/js/lib/main.js --- /dev/null +++ b/lib/galaxy/web/proxy/js/lib/main.js @@ -0,0 +1,41 @@ +#!/usr/bin/env node +/* +Inspiration taken from + https://github.com/jupyter/multiuser-server/blob/master/multiuser/js/main.js +*/ +var fs = require('fs'); +var args = require('commander'); + +package_info = require('../package') + +args + .version(package_info) + .option('--ip <n>', 'Public-facing IP of the proxy', 'localhost') + .option('--port <n>', 'Public-facing port of the proxy', parseInt) + .option('--cookie <cookiename>', 'Cookie proving authentication', 'galaxysession') + .option('--sessions <file>', 'Routes file to monitor') + .option('--verbose') + +args.parse(process.argv); + +var DynamicProxy = require('./proxy.js').DynamicProxy; +var mapFor = require('./mapper.js').mapFor; + +var sessions = mapFor(args.sessions); + +var dynamic_proxy_options = { + sessionCookie: args['cookie'], + sessionMap: sessions, + verbose: args.verbose +} + +var dynamic_proxy = new DynamicProxy(dynamic_proxy_options); + +var listen = {}; +listen.port = args.port || 8000; +listen.ip = args.ip; + +if(args.verbose) { + console.log("Listening on " + listen.ip + ":" + listen.port); +} +dynamic_proxy.proxy_server.listen(listen.port, listen.ip); diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/proxy/js/lib/mapper.js --- /dev/null +++ b/lib/galaxy/web/proxy/js/lib/mapper.js @@ -0,0 +1,78 @@ +var fs = require('fs'); +var sqlite3 = require('sqlite3') + + +var endsWith = function(subjectString, searchString) { + var position = subjectString.length; + position -= searchString.length; + var lastIndex = subjectString.indexOf(searchString, position); + return lastIndex !== -1 && lastIndex === position; +}; + + +var updateFromJson = function(path, map) { + var content = fs.readFileSync(path, 'utf8'); + var keyToSession = JSON.parse(content); + var newSessions = {}; + for(var key in keyToSession) { + var hostAndPort = key.split(":"); + // 'host': hostAndPort[0], + newSessions[keyToSession[key]] = {'target': {'host': hostAndPort[0], 'port': parseInt(hostAndPort[1])}}; + } + for(var oldSession in map) { + if(!(oldSession in newSessions)) { + delete map[ oldSession ]; + } + } + for(var newSession in newSessions) { + map[newSession] = newSessions[newSession]; + } +} + +var updateFromSqlite = function(path, map) { + var newSessions = {}; + var loadSessions = function() { + db.each("SELECT key, secret FROM gxproxy", function(err, row) { + var key = row['key']; + var secret = row['secret']; + var hostAndPort = key.split(":"); + var target = {'host': hostAndPort[0], 'port': parseInt(hostAndPort[1])}; + newSessions[secret] = {'target': target}; + }, finish); + }; + + var finish = function() { + for(var oldSession in map) { + if(!(oldSession in newSessions)) { + delete map[ oldSession ]; + } + } + for(var newSession in newSessions) { + map[newSession] = newSessions[newSession]; + } + db.close(); + }; + + var db = new sqlite3.Database(path, loadSessions); +}; + + +var mapFor = function(path) { + var map = {}; + var loadMap; + if(endsWith(path, '.sqlite')) { + loadMap = function() { + updateFromSqlite(path, map); + } + } else { + loadMap = function() { + updateFromJson(path, map); + } + } + console.log("Watching path " + path); + loadMap(); + fs.watch(path, loadMap); + return map; +}; + +exports.mapFor = mapFor; \ No newline at end of file diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/proxy/js/lib/proxy.js --- /dev/null +++ b/lib/galaxy/web/proxy/js/lib/proxy.js @@ -0,0 +1,119 @@ +var http = require('http'), + httpProxy = require('http-proxy'); + +var bound = function (that, method) { + // bind a method, to ensure `this=that` when it is called + // because prototype languages are bad + return function () { + method.apply(that, arguments); + }; +}; + +var DynamicProxy = function(options) { + var dynamicProxy = this; + this.sessionCookie = options.sessionCookie; + this.sessionMap = options.sessionMap; + this.debug = options.verbose; + + var log_errors = function(handler) { + return function (req, res) { + try { + return handler.apply(dynamicProxy, arguments); + } catch (e) { + console.log("Error in handler for " + req.method + ' ' + req.url + ': ', e); + } + }; + }; + + var proxy = this.proxy = httpProxy.createProxyServer({ + ws : true, + }); + + this.proxy_server = http.createServer( + log_errors(dynamicProxy.handleProxyRequest) + ); + this.proxy_server.on('upgrade', bound(this, this.handleWs)); +}; + +DynamicProxy.prototype.rewriteRequest = function(request) { +} + +DynamicProxy.prototype.targetForRequest = function(request) { + // return proxy target for a given url + var session = this.findSession(request); + for (var mappedSession in this.sessionMap) { + if(session == mappedSession) { + return this.sessionMap[session].target; + } + } + + return null; +}; + +DynamicProxy.prototype.findSession = function(request) { + var sessionCookie = this.sessionCookie; + rc = request.headers.cookie; + if(!rc) { + return null; + } + var cookies = rc.split(';'); + for(var cookieIndex in cookies) { + var cookie = cookies[cookieIndex]; + var parts = cookie.split('='); + var partName = parts.shift().trim(); + if(partName == sessionCookie) { + return unescape(parts.join('=')) + } + } + + return null; +}; + +DynamicProxy.prototype.handleProxyRequest = function(req, res) { + var target = this.targetForRequest(req); + if(this.debug) { + console.log("PROXY " + req.method + " " + req.url + " to " + target); + } + var origin = req.headers.origin; + this.rewriteRequest(req); + res.oldWriteHead = res.writeHead; + res.writeHead = function(statusCode, headers) { + res.setHeader('Access-Control-Allow-Origin', origin); + res.setHeader('Access-Control-Allow-Credentials', 'true'); + res.oldWriteHead(statusCode, headers); + } + this.proxy.web(req, res, { + target: target + }, function (e) { + console.log("Proxy error: ", e); + res.writeHead(502); + res.write("Proxy target missing"); + res.end(); + }); +}; + +DynamicProxy.prototype.handleWs = function(req, res, head) { + // no local route found, time to proxy + var target = this.targetForRequest(req); + if(this.debug) { + console.log("PROXY WS " + req.url + " to " + req.url); + } + var origin = req.headers.origin; + this.rewriteRequest(req); + res.oldWriteHead = res.writeHead; + res.writeHead = function(statusCode, headers) { + res.setHeader('Access-Control-Allow-Origin', origin); + res.setHeader('Access-Control-Allow-Credentials', 'true'); + res.oldWriteHead(statusCode, headers); + } + this.proxy.ws(req, res, head, { + target: target + }, function (e) { + console.log("Proxy error: ", e); + res.writeHead(502); + res.write("Proxy target missing"); + res.end(); + }); +}; + +exports.DynamicProxy = DynamicProxy; diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 lib/galaxy/web/proxy/js/package.json --- /dev/null +++ b/lib/galaxy/web/proxy/js/package.json @@ -0,0 +1,18 @@ +{ + "name": "galaxy-proxy", + "version": "0.0.1", + "description": "A dynamic reverse proxy for use within Galaxy", + "main": "index.js", + "author": "John Chilton", + "license": "AFL v3", + "readmeFilename": "README.md", + "repository": { + "type": "mercurial", + "url": "https://bitbucket.org/galaxy/galaxy-central" + }, + "dependencies": { + "http-proxy": "~1.1", + "commander": "~2.2", + "sqlite3": "3.0.2" + } +} diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 static/scripts/galaxy.interactive_environments.js --- /dev/null +++ b/static/scripts/galaxy.interactive_environments.js @@ -0,0 +1,59 @@ +/** + * Internal function to remove content from the main area and add the notebook. + * Not idempotent + */ +function append_notebook(url){ + clear_main_area(); + $('#main').append('<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:hidden;" scrolling="no" src="'+ url +'"></iframe>' + ); +} + +function clear_main_area(){ + $('#spinner').remove(); + $('#main').children().remove(); +} + +function display_spinner(){ + $('#main').append('<img id="spinner" src="' + galaxy_root + '/static/style/largespinner.gif" style="position:absolute;margin:auto;top:0;left:0;right:0;bottom:0;">'); +} + + +/** + * Test availability of a URL, and call a callback when done. + * http://stackoverflow.com/q/25390206/347368 + * @param {String} url: URL to test availability of. Must return a 200 (302->200 is OK). + * @param {String} callback: function to call once successfully connected. + * + */ +function test_ie_availability(url, success_callback){ + var request_count = 0; + display_spinner(); + interval = setInterval(function(){ + $.ajax({ + url: url, + xhrFields: { + withCredentials: true + }, + type: "GET", + timeout: 500, + success: function(){ + console.log("Connected to IE, returning"); + clearInterval(interval); + success_callback(); + }, + error: function(jqxhr, status, error){ + request_count++; + console.log("Request " + request_count); + if(request_count > 30){ + clearInterval(interval); + clear_main_area(); + toastr.error( + "Could not connect to IE, contact your administrator", + "Error", + {'closeButton': true, 'timeOut': 20000, 'tapToDismiss': false} + ); + } + } + }); + }, 1000); +} diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 static/scripts/packed/galaxy.interactive_environments.js --- /dev/null +++ b/static/scripts/packed/galaxy.interactive_environments.js @@ -0,0 +1,1 @@ +function append_notebook(a){clear_main_area();$("#main").append('<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:hidden;" scrolling="no" src="'+a+'"></iframe>')}function clear_main_area(){$("#spinner").remove();$("#main").children().remove()}function display_spinner(){$("#main").append('<img id="spinner" src="'+galaxy_root+'/static/style/largespinner.gif" style="position:absolute;margin:auto;top:0;left:0;right:0;bottom:0;">')}function test_ie_availability(b,c){var a=0;display_spinner();interval=setInterval(function(){$.ajax({url:b,xhrFields:{withCredentials:true},type:"GET",timeout:500,success:function(){console.log("Connected to IE, returning");clearInterval(interval);c()},error:function(f,d,e){a++;console.log("Request "+a);if(a>30){clearInterval(interval);clear_main_area();toastr.error("Could not connect to IE, contact your administrator","Error",{closeButton:true,timeOut:20000,tapToDismiss:false})}}})},1000)}; \ No newline at end of file diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 test/unit/test_lazy_process.py --- /dev/null +++ b/test/unit/test_lazy_process.py @@ -0,0 +1,19 @@ +import os +import tempfile +import time + +from galaxy.util.lazy_process import LazyProcess + + +def test_lazy_process(): + t = tempfile.NamedTemporaryFile() + os.remove(t.name) + lazy_process = LazyProcess(["bash", "-c", "touch %s; sleep 100" % t.name]) + assert not os.path.exists(t.name) + lazy_process.start_process() + time.sleep(.02) + assert lazy_process.process.poll() is None + assert os.path.exists(t.name) + lazy_process.shutdown() + time.sleep(.02) + assert lazy_process.process.poll() diff -r 35c1392b049cbf41844be1fcf2d055f8314e16ae -r 70f7ff8c6a96ede6e439beb62d64152cc5ad2b04 test/unit/test_sockets.py --- /dev/null +++ b/test/unit/test_sockets.py @@ -0,0 +1,12 @@ +import socket +from galaxy.util import sockets + + +def test_unused_free_port_unconstrained(): + port = sockets.unused_port() + + s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) + # would throw exception if port was not free. + s.bind(('localhost', port)) + s.close() + 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: dannon: Move handler startup to immediately following full creation and association of the JobManager.
by commits-noreply＠bitbucket.org 20 Oct '14

20 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a7b2aabb27ff/ Changeset: a7b2aabb27ff Branch: stable User: dannon Date: 2014-10-15 14:21:13+00:00 Summary: Move handler startup to immediately following full creation and association of the JobManager. Affected #: 2 files diff -r 78c9a97be4b6bfe55136b055477fd1b9f22fd848 -r a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -134,6 +134,7 @@ # Start the job manager from galaxy.jobs import manager self.job_manager = manager.JobManager( self ) + self.job_manager.start() # FIXME: These are exposed directly for backward compatibility self.job_queue = self.job_manager.job_queue self.job_stop_queue = self.job_manager.job_stop_queue diff -r 78c9a97be4b6bfe55136b055477fd1b9f22fd848 -r a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -27,6 +27,8 @@ self.job_handler = NoopHandler() self.job_queue = self.job_stop_queue = NoopQueue() self.job_lock = False + + def start( self ): self.job_handler.start() def shutdown( self ): 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: Fix to 875056d: correct selector bleed in subtitle
by commits-noreply＠bitbucket.org 20 Oct '14

20 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/35c1392b049c/ Changeset: 35c1392b049c User: carlfeberhard Date: 2014-10-20 14:48:45+00:00 Summary: Fix to 875056d: correct selector bleed in subtitle Affected #: 3 files diff -r 720ea1796c26574d642e02db3583085c348a4474 -r 35c1392b049cbf41844be1fcf2d055f8314e16ae client/galaxy/scripts/mvc/history/history-panel-edit.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit.js @@ -148,7 +148,7 @@ :( toggleLink( 'toggle-hidden-link', _l( 'hide hidden' ) ) ) ); } - return $whereTo.find( '.subtitle' ).html( msgs.join( ', ' ) ); + return $whereTo.find( '> .controls .subtitle' ).html( msgs.join( ', ' ) ); }, /** render the tags sub-view controller */ diff -r 720ea1796c26574d642e02db3583085c348a4474 -r 35c1392b049cbf41844be1fcf2d055f8314e16ae static/scripts/mvc/history/history-panel-edit.js --- a/static/scripts/mvc/history/history-panel-edit.js +++ b/static/scripts/mvc/history/history-panel-edit.js @@ -148,7 +148,7 @@ :( toggleLink( 'toggle-hidden-link', _l( 'hide hidden' ) ) ) ); } - return $whereTo.find( '.subtitle' ).html( msgs.join( ', ' ) ); + return $whereTo.find( '> .controls .subtitle' ).html( msgs.join( ', ' ) ); }, /** render the tags sub-view controller */ diff -r 720ea1796c26574d642e02db3583085c348a4474 -r 35c1392b049cbf41844be1fcf2d055f8314e16ae static/scripts/packed/mvc/history/history-panel-edit.js --- a/static/scripts/packed/mvc/history/history-panel-edit.js +++ b/static/scripts/packed/mvc/history/history-panel-edit.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","utils/localization"],function(f,h,k,d,c,g,j,a,b){var i=f.HistoryPanel;var e=i.extend({HDAViewClass:c.HDAListItemEdit,HDCAViewClass:g.HDCAListItemEdit,initialize:function(l){l=l||{};i.prototype.initialize.call(this,l);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=l.purgeAllowed||false;this.annotationEditorShown=l.annotationEditorShown||false;this.tagsEditorShown=l.tagsEditorShown||false;this.multiselectActions=l.multiselectActions||this._getActions()},_setUpListeners:function(){i.prototype._setUpListeners.call(this);this.on("drop",function(l,m){this.dataDropped(m);this.dropTargetOff()})},_setUpCollectionListeners:function(){i.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(l){this.model.fetch()},this);return this},_setUpModelListeners:function(){i.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var l=i.prototype._buildNewRender.call(this);if(!this.model){return l}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(l);this._renderAnnotation(l)}return l},renderItems:function(m){var l=i.prototype.renderItems.call(this,m);this._renderCounts(m);return l},_renderCounts:function(n){function m(q,r){return['<a class="',q,'" href="javascript:void(0);">',r,"</a>"].join("")}n=n||this.$el;var l=this.collection.where({deleted:true}),p=this.collection.where({visible:false}),o=[];if(this.views.length){o.push([this.views.length,b("shown")].join(" "))}if(l.length){o.push((!this.showDeleted)?([l.length,m("toggle-deleted-link",b("deleted"))].join(" ")):(m("toggle-deleted-link",b("hide deleted"))))}if(p.length){o.push((!this.showHidden)?([p.length,m("toggle-hidden-link",b("hidden"))].join(" ")):(m("toggle-hidden-link",b("hide hidden"))))}return n.find(".subtitle").html(o.join(", "))},_renderTags:function(l){var m=this;this.tagsEditor=new j.TagsEditor({model:this.model,el:l.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDATagEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDATagEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(l.find(".controls .actions"))})},_renderAnnotation:function(l){var m=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:l.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDAAnnotationEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDAAnnotationEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(l.find(".controls .actions"))})},_setUpBehaviors:function(l){l=l||this.$el;i.prototype._setUpBehaviors.call(this,l);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new PopupMenu(l.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var m=this,n=".controls .name";l.find(n).attr("title",b("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(o){var p=m.model.get("name");if(o&&o!==p){m.$el.find(n).text(o);m.model.save({name:o}).fail(function(){m.$el.find(n).text(m.model.previous("name"))})}else{m.$el.find(n).text(p)}}})},_getActions:function(){var l=this,m=[{html:b("Hide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.hide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Unhide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.unhide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Delete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype["delete"];l.getSelectedModels().ajaxQueue(n)}},{html:b("Undelete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.undelete;l.getSelectedModels().ajaxQueue(n)}}];if(l.purgeAllowed){m.push({html:b("Permanently delete datasets"),func:function(){if(confirm(b("This will permanently remove the data in your datasets. Are you sure?"))){var n=d.HistoryDatasetAssociation.prototype.purge;l.getSelectedModels().ajaxQueue(n)}}})}m.push({html:b("Build Dataset List"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"list")}});m.push({html:b("Build Dataset Pair"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"paired")}});m.push({html:b("Build List of Dataset Pairs"),func:_.bind(l._showPairedCollectionModal,l)});return m},_showPairedCollectionModal:function(){var l=this,m=l.getSelectedModels().toJSON().filter(function(n){return n.history_content_type==="dataset"&&n.state===k.OK});if(m.length){require(["mvc/collection/paired-collection-creator"],function(n){window.creator=n.pairedCollectionCreatorModal(m,{historyId:l.model.id})})}else{}},_attachItems:function(l){this.$list(l).append(this.views.reverse().map(function(m){return m.$el}));return this},_attachView:function(m){var l=this;l.views.unshift(m);l.$list().prepend(m.render(0).$el.hide());m.$el.slideDown(l.fxSpeed)},_getItemViewOptions:function(m){var l=i.prototype._getItemViewOptions.call(this,m);_.extend(l,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return l},_handleHdaDeletionChange:function(l){this._renderCounts();if(l.get("deleted")&&!this.showDeleted){this.removeItemView(l)}},_handleHdaVisibleChange:function(l){this._renderCounts();if(l.hidden()&&!this.storage.showHidden){this.removeItemView(l)}},toggleHDATagEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.tagsEditor){n.tagsEditor.toggle.apply(n.tagsEditor,m)}})},toggleHDAAnnotationEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.annotationEditor){n.annotationEditor.toggle.apply(n.annotationEditor,m)}})},events:_.extend(_.clone(i.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(l){this.toggleShowDeleted()},"click .toggle-hidden-link":function(l){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var m={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var n=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),n]);for(var l in m){if(m.hasOwnProperty(l)){n.on(l,m[l])}}return this},_renderDropTarget:function(){return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(b("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(l){l.preventDefault();l.stopPropagation()},dragleave:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(n){n.preventDefault();n.dataTransfer.dropEffect="move";var l=this,o=n.dataTransfer.getData("text");try{o=JSON.parse(o)}catch(m){this.warn("error parsing JSON from drop:",o)}this.trigger("droptarget:drop",n,o,l);return false},dataDropped:function(m){var l=this;if(_.isObject(m)&&m.model_class==="HistoryDatasetAssociation"&&m.id){return l.model.contents.copy(m.id)}return jQuery.when()},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:e}}); \ No newline at end of file +define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","utils/localization"],function(f,h,k,d,c,g,j,a,b){var i=f.HistoryPanel;var e=i.extend({HDAViewClass:c.HDAListItemEdit,HDCAViewClass:g.HDCAListItemEdit,initialize:function(l){l=l||{};i.prototype.initialize.call(this,l);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=l.purgeAllowed||false;this.annotationEditorShown=l.annotationEditorShown||false;this.tagsEditorShown=l.tagsEditorShown||false;this.multiselectActions=l.multiselectActions||this._getActions()},_setUpListeners:function(){i.prototype._setUpListeners.call(this);this.on("drop",function(l,m){this.dataDropped(m);this.dropTargetOff()})},_setUpCollectionListeners:function(){i.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(l){this.model.fetch()},this);return this},_setUpModelListeners:function(){i.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var l=i.prototype._buildNewRender.call(this);if(!this.model){return l}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(l);this._renderAnnotation(l)}return l},renderItems:function(m){var l=i.prototype.renderItems.call(this,m);this._renderCounts(m);return l},_renderCounts:function(n){function m(q,r){return['<a class="',q,'" href="javascript:void(0);">',r,"</a>"].join("")}n=n||this.$el;var l=this.collection.where({deleted:true}),p=this.collection.where({visible:false}),o=[];if(this.views.length){o.push([this.views.length,b("shown")].join(" "))}if(l.length){o.push((!this.showDeleted)?([l.length,m("toggle-deleted-link",b("deleted"))].join(" ")):(m("toggle-deleted-link",b("hide deleted"))))}if(p.length){o.push((!this.showHidden)?([p.length,m("toggle-hidden-link",b("hidden"))].join(" ")):(m("toggle-hidden-link",b("hide hidden"))))}return n.find("> .controls .subtitle").html(o.join(", "))},_renderTags:function(l){var m=this;this.tagsEditor=new j.TagsEditor({model:this.model,el:l.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDATagEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDATagEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(l.find(".controls .actions"))})},_renderAnnotation:function(l){var m=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:l.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDAAnnotationEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDAAnnotationEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(l.find(".controls .actions"))})},_setUpBehaviors:function(l){l=l||this.$el;i.prototype._setUpBehaviors.call(this,l);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new PopupMenu(l.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var m=this,n=".controls .name";l.find(n).attr("title",b("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(o){var p=m.model.get("name");if(o&&o!==p){m.$el.find(n).text(o);m.model.save({name:o}).fail(function(){m.$el.find(n).text(m.model.previous("name"))})}else{m.$el.find(n).text(p)}}})},_getActions:function(){var l=this,m=[{html:b("Hide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.hide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Unhide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.unhide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Delete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype["delete"];l.getSelectedModels().ajaxQueue(n)}},{html:b("Undelete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.undelete;l.getSelectedModels().ajaxQueue(n)}}];if(l.purgeAllowed){m.push({html:b("Permanently delete datasets"),func:function(){if(confirm(b("This will permanently remove the data in your datasets. Are you sure?"))){var n=d.HistoryDatasetAssociation.prototype.purge;l.getSelectedModels().ajaxQueue(n)}}})}m.push({html:b("Build Dataset List"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"list")}});m.push({html:b("Build Dataset Pair"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"paired")}});m.push({html:b("Build List of Dataset Pairs"),func:_.bind(l._showPairedCollectionModal,l)});return m},_showPairedCollectionModal:function(){var l=this,m=l.getSelectedModels().toJSON().filter(function(n){return n.history_content_type==="dataset"&&n.state===k.OK});if(m.length){require(["mvc/collection/paired-collection-creator"],function(n){window.creator=n.pairedCollectionCreatorModal(m,{historyId:l.model.id})})}else{}},_attachItems:function(l){this.$list(l).append(this.views.reverse().map(function(m){return m.$el}));return this},_attachView:function(m){var l=this;l.views.unshift(m);l.$list().prepend(m.render(0).$el.hide());m.$el.slideDown(l.fxSpeed)},_getItemViewOptions:function(m){var l=i.prototype._getItemViewOptions.call(this,m);_.extend(l,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return l},_handleHdaDeletionChange:function(l){this._renderCounts();if(l.get("deleted")&&!this.showDeleted){this.removeItemView(l)}},_handleHdaVisibleChange:function(l){this._renderCounts();if(l.hidden()&&!this.storage.showHidden){this.removeItemView(l)}},toggleHDATagEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.tagsEditor){n.tagsEditor.toggle.apply(n.tagsEditor,m)}})},toggleHDAAnnotationEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.annotationEditor){n.annotationEditor.toggle.apply(n.annotationEditor,m)}})},events:_.extend(_.clone(i.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(l){this.toggleShowDeleted()},"click .toggle-hidden-link":function(l){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var m={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var n=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),n]);for(var l in m){if(m.hasOwnProperty(l)){n.on(l,m[l])}}return this},_renderDropTarget:function(){return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(b("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(l){l.preventDefault();l.stopPropagation()},dragleave:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(n){n.preventDefault();n.dataTransfer.dropEffect="move";var l=this,o=n.dataTransfer.getData("text");try{o=JSON.parse(o)}catch(m){this.warn("error parsing JSON from drop:",o)}this.trigger("droptarget:drop",n,o,l);return false},dataDropped:function(m){var l=this;if(_.isObject(m)&&m.model_class==="HistoryDatasetAssociation"&&m.id){return l.model.contents.copy(m.id)}return jQuery.when()},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] 566fdc: cleanup of tool_conf.xml
by GitHub 17 Oct '14

17 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 566fdc97d83df8b74597e6e8b752a34ca6465599 https://github.com/galaxyproject/usegalaxy-playbook/commit/566fdc97d83df8b7… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2014-10-17 (Fri, 17 Oct 2014) Changed paths: M files/galaxy/test.galaxyproject.org/config/tool_conf.xml Log Message: ----------- cleanup of tool_conf.xml

1 0

commit/galaxy-central: guerler: ToolForm: Improve validation
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/720ea1796c26/ Changeset: 720ea1796c26 User: guerler Date: 2014-10-17 18:11:25+00:00 Summary: ToolForm: Improve validation Affected #: 3 files diff -r d8163f6a8f51ffb44fc8858ae8714f41226d93f8 -r 720ea1796c26574d642e02db3583085c348a4474 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -96,7 +96,8 @@ var job_inputs = job_def.inputs; // counter for values declared in batch mode - var n_values = -1; + var batch_n = -1; + var batch_src = null; // validation for (var job_input_id in job_inputs) { @@ -116,12 +117,33 @@ // check if input field is in batch mode if (input_value.batch) { + // get values var n = input_value.values.length; - if (n_values === -1) { - n_values = n; + + // get source + var src = null; + if (n > 0) { + src = input_value.values[0] && input_value.values[0].src; + } + + // check source type + if (src) { + if (batch_src === null) { + batch_src = src; + } else { + if (batch_src !== src) { + this._foundError(input_id, 'Please select either dataset or dataset list fields for all batch mode fields.'); + return false; + } + } + } + + // check number of inputs + if (batch_n === -1) { + batch_n = n; } else { - if (n_values !== n) { - this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); return false; } } diff -r d8163f6a8f51ffb44fc8858ae8714f41226d93f8 -r 720ea1796c26574d642e02db3583085c348a4474 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -96,7 +96,8 @@ var job_inputs = job_def.inputs; // counter for values declared in batch mode - var n_values = -1; + var batch_n = -1; + var batch_src = null; // validation for (var job_input_id in job_inputs) { @@ -116,12 +117,33 @@ // check if input field is in batch mode if (input_value.batch) { + // get values var n = input_value.values.length; - if (n_values === -1) { - n_values = n; + + // get source + var src = null; + if (n > 0) { + src = input_value.values[0] && input_value.values[0].src; + } + + // check source type + if (src) { + if (batch_src === null) { + batch_src = src; + } else { + if (batch_src !== src) { + this._foundError(input_id, 'Please select either dataset or dataset list fields for all batch mode fields.'); + return false; + } + } + } + + // check number of inputs + if (batch_n === -1) { + batch_n = n; } else { - if (n_values !== n) { - this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); return false; } } diff -r d8163f6a8f51ffb44fc8858ae8714f41226d93f8 -r 720ea1796c26574d642e02db3583085c348a4474 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(j&&e&&e.validate&&!e.validate()){this._foundError(l);return false}if(f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ 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: guerler: ToolForm: Fix collection selection
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d8163f6a8f51/ Changeset: d8163f6a8f51 User: guerler Date: 2014-10-17 17:52:21+00:00 Summary: ToolForm: Fix collection selection Affected #: 3 files diff -r 7cc092b92c966053f134caf7ef60077da2349486 -r d8163f6a8f51ffb44fc8858ae8714f41226d93f8 client/galaxy/scripts/mvc/tools/tools-content.js --- a/client/galaxy/scripts/mvc/tools/tools-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-content.js @@ -72,7 +72,7 @@ var content = this.summary[i]; // check ok state (TODO: should be implemented in the api) - if (content.state !== 'ok') { + if (content.history_content_type === 'dataset' && content.state !== 'ok') { continue; } diff -r 7cc092b92c966053f134caf7ef60077da2349486 -r d8163f6a8f51ffb44fc8858ae8714f41226d93f8 static/scripts/mvc/tools/tools-content.js --- a/static/scripts/mvc/tools/tools-content.js +++ b/static/scripts/mvc/tools/tools-content.js @@ -72,7 +72,7 @@ var content = this.summary[i]; // check ok state (TODO: should be implemented in the api) - if (content.state !== 'ok') { + if (content.history_content_type === 'dataset' && content.state !== 'ok') { continue; } diff -r 7cc092b92c966053f134caf7ef60077da2349486 -r d8163f6a8f51ffb44fc8858ae8714f41226d93f8 static/scripts/packed/mvc/tools/tools-content.js --- a/static/scripts/packed/mvc/tools/tools-content.js +++ b/static/scripts/packed/mvc/tools/tools-content.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;b.summary.sort(function(g,f){return g.hid>f.hid?-1:(g.hid<f.hid?1:0)});console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];if(e.state!=="ok"){continue}var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;b.summary.sort(function(g,f){return g.hid>f.hid?-1:(g.hid<f.hid?1:0)});console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];if(e.history_content_type==="dataset"&&e.state!=="ok"){continue}var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Improve dataset filtering
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7cc092b92c96/ Changeset: 7cc092b92c96 User: guerler Date: 2014-10-17 17:32:24+00:00 Summary: ToolForm: Improve dataset filtering Affected #: 12 files diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 client/galaxy/scripts/mvc/tools/tools-content.js --- a/client/galaxy/scripts/mvc/tools/tools-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-content.js @@ -22,7 +22,7 @@ // get history summary Utils.get({ - url : self.base_url + '?deleted=false&state=ok', + url : self.base_url + '?deleted=false', success : function(response) { // backup summary self.summary = response; @@ -71,6 +71,11 @@ for (var i in this.summary) { var content = this.summary[i]; + // check ok state (TODO: should be implemented in the api) + if (content.state !== 'ok') { + continue; + } + // match datatypes var found = false; for (var i in options.extensions) { diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -126,6 +126,12 @@ this.select_collection.value(list[0]); break; } + + // check if value has been set + var select = this._select(); + if (!select.validate()) { + select.value(select.first()); + } } catch (err) { console.debug('tools-select-content::value() - Skipped.'); } diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -114,7 +114,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null') { + if ([null, 'null', undefined].indexOf(current[i]) > -1) { return false; } } diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -91,7 +91,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null') { + if ([null, 'null', undefined].indexOf(current[i]) > -1) { return false; } } diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 static/scripts/mvc/tools/tools-content.js --- a/static/scripts/mvc/tools/tools-content.js +++ b/static/scripts/mvc/tools/tools-content.js @@ -22,7 +22,7 @@ // get history summary Utils.get({ - url : self.base_url + '?deleted=false&state=ok', + url : self.base_url + '?deleted=false', success : function(response) { // backup summary self.summary = response; @@ -71,6 +71,11 @@ for (var i in this.summary) { var content = this.summary[i]; + // check ok state (TODO: should be implemented in the api) + if (content.state !== 'ok') { + continue; + } + // match datatypes var found = false; for (var i in options.extensions) { diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -126,6 +126,12 @@ this.select_collection.value(list[0]); break; } + + // check if value has been set + var select = this._select(); + if (!select.validate()) { + select.value(select.first()); + } } catch (err) { console.debug('tools-select-content::value() - Skipped.'); } diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -114,7 +114,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null') { + if ([null, 'null', undefined].indexOf(current[i]) > -1) { return false; } } diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -91,7 +91,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null') { + if ([null, 'null', undefined].indexOf(current[i]) > -1) { return false; } } diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 static/scripts/packed/mvc/tools/tools-content.js --- a/static/scripts/packed/mvc/tools/tools-content.js +++ b/static/scripts/packed/mvc/tools/tools-content.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false&state=ok",success:function(e){b.summary=e;b.summary.sort(function(g,f){return g.hid>f.hid?-1:(g.hid<f.hid?1:0)});console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;b.summary.sort(function(g,f){return g.hid>f.hid?-1:(g.hid<f.hid?1:0)});console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];if(e.state!=="ok"){continue}var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ No newline at end of file diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.content.filterType({src:"hda",extensions:h.extensions});var k=[];for(var j in l){k.push({label:l[j].hid+": "+l[j].name,value:l[j].id})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.content.filterType({src:"hdca",extensions:h.extensions});var f=[];for(var j in m){f.push({label:m[j].hid+": "+m[j].name,value:m[j].id})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(l){if(l!==undefined){try{this.current=l.values[0].src;this.refresh();var k=[];for(var g in l.values){k.push(l.values[g].id)}switch(this.current){case"hda":this.select_datasets.value(k);break;case"hdca":this.select_collection.value(k[0]);break}}catch(j){console.debug("tools-select-content::value() - Skipped.")}}var h=this._select().value();if(!(h instanceof Array)){h=[h]}var f={batch:!this.options.multiple,values:[]};for(var g in h){f.values.push({id:h[g],src:this.current})}return f},validate:function(){return this._select().validate()},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}},_select:function(){switch(this.current){case"hdca":return this.select_collection;default:return this.select_datasets}}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.content.filterType({src:"hda",extensions:h.extensions});var k=[];for(var j in l){k.push({label:l[j].hid+": "+l[j].name,value:l[j].id})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.content.filterType({src:"hdca",extensions:h.extensions});var f=[];for(var j in m){f.push({label:m[j].hid+": "+m[j].name,value:m[j].id})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(m){if(m!==undefined){try{this.current=m.values[0].src;this.refresh();var l=[];for(var h in m.values){l.push(m.values[h].id)}switch(this.current){case"hda":this.select_datasets.value(l);break;case"hdca":this.select_collection.value(l[0]);break}var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.current})}return f},validate:function(){return this._select().validate()},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}},_select:function(){switch(this.current){case"hdca":return this.select_collection;default:return this.select_datasets}}});return{View:d}}); \ No newline at end of file diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$error=$(this._templateError(g));this.$options=$(this._template(g));this.$el.append(this.$error);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if(g[f]==="null"){return false}}return true},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){var f=this.$el.find(".ui-option").length;if(f==0){this.$error.show();this.$options.hide()}else{this.$error.hide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_templateError:function(f){return'<div class="ui-error" style="display: none;">'+f.empty+"</div>"}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$error=$(this._templateError(g));this.$options=$(this._template(g));this.$el.append(this.$error);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){var f=this.$el.find(".ui-option").length;if(f==0){this.$error.show();this.$options.hide()}else{this.$error.hide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_templateError:function(f){return'<div class="ui-error" style="display: none;">'+f.empty+"</div>"}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 -r 7cc092b92c966053f134caf7ef60077da2349486 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if(d[c]==="null"){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: History panel: fix 'load you own data' link to Galaxy.upload
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d5f495c94ba1/ Changeset: d5f495c94ba1 User: carlfeberhard Date: 2014-10-17 16:37:45+00:00 Summary: History panel: fix 'load you own data' link to Galaxy.upload Affected #: 3 files diff -r db0a3f2a952e1ee0a6f76c5355346b23f9166330 -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 client/galaxy/scripts/mvc/history/history-panel-edit-current.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js @@ -226,7 +226,7 @@ '</a>' ].join('') ); $emptyMsg.find( '.uploader-link' ).click( function( ev ){ - Galaxy.upload._eventShow( ev ); + Galaxy.upload.show( ev ); }); $emptyMsg.find( '.get-data-link' ).click( function( ev ){ $toolMenu.parent().scrollTop( 0 ); diff -r db0a3f2a952e1ee0a6f76c5355346b23f9166330 -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 static/scripts/mvc/history/history-panel-edit-current.js --- a/static/scripts/mvc/history/history-panel-edit-current.js +++ b/static/scripts/mvc/history/history-panel-edit-current.js @@ -226,7 +226,7 @@ '</a>' ].join('') ); $emptyMsg.find( '.uploader-link' ).click( function( ev ){ - Galaxy.upload._eventShow( ev ); + Galaxy.upload.show( ev ); }); $emptyMsg.find( '.get-data-link' ).click( function( ev ){ $toolMenu.parent().scrollTop( 0 ); diff -r db0a3f2a952e1ee0a6f76c5355346b23f9166330 -r d5f495c94ba1d558e492b2f9bae2b78b672cae66 static/scripts/packed/mvc/history/history-panel-edit-current.js --- a/static/scripts/packed/mvc/history/history-panel-edit-current.js +++ b/static/scripts/packed/mvc/history/history-panel-edit-current.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){if(j.$el.is(":visible")){j.preferences.set("scrollPosition",$(this).scrollTop())}});this.on("new-model",function(){j.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){g.prototype._attachItems.call(this,k);var j=this,l;if(j.currentContentId&&(l=j.viewFromModelId(j.currentContentId))){j.setCurrentContent(l)}return this},addItemView:function(l,m,k){var j=g.prototype.addItemView.call(this,l,m,k);if(!j){return j}if(this.panelStack.length){return this._collapseDrilldownPanel()}return j},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){var k=this;if(!j){return k}this.on("new-storage show-deleted show-hidden",function(){var l=(Galaxy&&Galaxy.historyOptionsMenu)?Galaxy.historyOptionsMenu:undefined;if(l){l.findItemByHtml(b("Include Deleted Datasets")).checked=k.showDeleted;l.findItemByHtml(b("Include Hidden Datasets")).checked=k.showHidden}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){if(j.$el.is(":visible")){j.preferences.set("scrollPosition",$(this).scrollTop())}});this.on("new-model",function(){j.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload.show(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){g.prototype._attachItems.call(this,k);var j=this,l;if(j.currentContentId&&(l=j.viewFromModelId(j.currentContentId))){j.setCurrentContent(l)}return this},addItemView:function(l,m,k){var j=g.prototype.addItemView.call(this,l,m,k);if(!j){return j}if(this.panelStack.length){return this._collapseDrilldownPanel()}return j},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){var k=this;if(!j){return k}this.on("new-storage show-deleted show-hidden",function(){var l=(Galaxy&&Galaxy.historyOptionsMenu)?Galaxy.historyOptionsMenu:undefined;if(l){l.findItemByHtml(b("Include Deleted Datasets")).checked=k.showDeleted;l.findItemByHtml(b("Include Hidden Datasets")).checked=k.showHidden}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Parameters: Add validation
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/db0a3f2a952e/ Changeset: db0a3f2a952e User: guerler Date: 2014-10-17 14:03:13+00:00 Summary: Parameters: Add validation Affected #: 1 file diff -r acb838d9af911cfc7c79328ffa87472913e5529c -r db0a3f2a952e1ee0a6f76c5355346b23f9166330 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1163,8 +1163,9 @@ @staticmethod def _strip_c(column): - if column.startswith( 'c' ): - column = column.strip().lower()[1:] + if isinstance(column, basestring): + if column.startswith( 'c' ): + column = column.strip().lower()[1:] return column def get_column_list( self, trans, other_values ): 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

[galaxyproject/usegalaxy-playbook] cf32b4: Dropped survey slide; added training network slide...
by GitHub 17 Oct '14

17 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cf32b45543bd46b62761071bc2af8ca73906ea07 https://github.com/galaxyproject/usegalaxy-playbook/commit/cf32b45543bd46b6… Author: Dave Clements <clements(a)Dave-Clementss-MacBook-Pro.local> Date: 2014-10-17 (Fri, 17 Oct 2014) Changed paths: A files/galaxy/common/static/welcome_img/GTN.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped survey slide; added training network slide.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 17 Oct '14

17 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3d030de0c470/ Changeset: 3d030de0c470 User: dannon Date: 2014-10-17 12:07:24+00:00 Summary: Merge stable. Affected #: 3 files diff -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef -r 3d030de0c4708214f7add0c6391e0bd9024c045a .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -cb0c2ea402e4c82c7872177e874ce59de29c9c13 latest_2014.10.06 +e1404e285ccb9e52bd09c5827934cd0da1974acc latest_2014.10.06 diff -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef -r 3d030de0c4708214f7add0c6391e0bd9024c045a lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1336,6 +1336,7 @@ self.purged = False self.purgable = purgable self.external_filename = external_filename + self.external_extra_files_path = None self._extra_files_path = extra_files_path self.file_size = file_size if uuid is None: @@ -1359,9 +1360,20 @@ else: self.external_filename = filename file_name = property( get_file_name, set_file_name ) - @property - def extra_files_path( self ): - return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id ) + def get_extra_files_path( self ): + # Unlike get_file_name - extrnal_extra_files_path is not backed by an + # actual database column so if SA instantiates this object - the + # attribute won't exist yet. + if not getattr( self, "external_extra_files_path", None ): + return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id ) + else: + return os.path.abspath( self.external_extra_files_path ) + def set_extra_files_path( self, extra_files_path ): + if not extra_files_path: + self.external_extra_files_path = None + else: + self.external_extra_files_path = extra_files_path + extra_files_path = property( get_extra_files_path, set_extra_files_path) def _calculate_size( self ): if self.external_filename: try: diff -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef -r 3d030de0c4708214f7add0c6391e0bd9024c045a scripts/set_metadata.py --- a/scripts/set_metadata.py +++ b/scripts/set_metadata.py @@ -110,6 +110,8 @@ dataset = cPickle.load( open( filename_in ) ) # load DatasetInstance if dataset_filename_override: dataset.dataset.external_filename = dataset_filename_override + files_path = os.path.abspath(os.path.join( tool_job_working_directory, "dataset_%s_files" % (dataset.dataset.id) )) + dataset.dataset.external_extra_files_path = files_path if dataset.dataset.id in existing_job_metadata_dict: dataset.extension = existing_job_metadata_dict[ dataset.dataset.id ].get( 'ext', dataset.extension ) # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles https://bitbucket.org/galaxy/galaxy-central/commits/acb838d9af91/ Changeset: acb838d9af91 User: dannon Date: 2014-10-17 12:08:08+00:00 Summary: Fix typo noticed by nsoranzo. Affected #: 1 file diff -r 3d030de0c4708214f7add0c6391e0bd9024c045a -r acb838d9af911cfc7c79328ffa87472913e5529c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1361,7 +1361,7 @@ self.external_filename = filename file_name = property( get_file_name, set_file_name ) def get_extra_files_path( self ): - # Unlike get_file_name - extrnal_extra_files_path is not backed by an + # Unlike get_file_name - external_extra_files_path is not backed by an # actual database column so if SA instantiates this object - the # attribute won't exist yet. if not getattr( self, "external_extra_files_path", None ): @@ -2449,7 +2449,7 @@ file_size = int( ldda.get_size() ) except OSError: file_size = 0 - + rval = dict( id = ldda.id, hda_ldda = 'ldda', model_class = self.__class__.__name__, 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: Upload: Handle ftp api errors on client side
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0e8235a516d1/ Changeset: 0e8235a516d1 User: guerler Date: 2014-10-16 23:59:08+00:00 Summary: Upload: Handle ftp api errors on client side Affected #: 4 files diff -r d404a6f6d01e6af5cbd35a427c474cee47fe963a -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef client/galaxy/scripts/mvc/upload/upload-ftp.js --- a/client/galaxy/scripts/mvc/upload/upload-ftp.js +++ b/client/galaxy/scripts/mvc/upload/upload-ftp.js @@ -23,7 +23,8 @@ // load extension Utils.get({ url : galaxy_config.root + 'api/ftp_files', - success : function(ftp_files) { self._fill(ftp_files); } + success : function(ftp_files) { self._fill(ftp_files); }, + error : function() { self._fill(); } }); }, @@ -34,7 +35,7 @@ // fill table _fill: function(ftp_files) { - if (ftp_files.length > 0) { + if (ftp_files && ftp_files.length > 0) { // add table this.$el.find('#upload-ftp-content').html($(this._templateTable())); diff -r d404a6f6d01e6af5cbd35a427c474cee47fe963a -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef lib/galaxy/webapps/galaxy/api/ftp_files.py --- a/lib/galaxy/webapps/galaxy/api/ftp_files.py +++ b/lib/galaxy/webapps/galaxy/api/ftp_files.py @@ -112,7 +112,8 @@ response.append( dict( path = path, size = statinfo.st_size, ctime = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) - + else: + raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' ) # sort by path response = sorted(response, key=itemgetter("path")) return response diff -r d404a6f6d01e6af5cbd35a427c474cee47fe963a -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef static/scripts/mvc/upload/upload-ftp.js --- a/static/scripts/mvc/upload/upload-ftp.js +++ b/static/scripts/mvc/upload/upload-ftp.js @@ -23,7 +23,8 @@ // load extension Utils.get({ url : galaxy_config.root + 'api/ftp_files', - success : function(ftp_files) { self._fill(ftp_files); } + success : function(ftp_files) { self._fill(ftp_files); }, + error : function() { self._fill(); } }); }, @@ -34,7 +35,7 @@ // fill table _fill: function(ftp_files) { - if (ftp_files.length > 0) { + if (ftp_files && ftp_files.length > 0) { // add table this.$el.find('#upload-ftp-content').html($(this._templateTable())); diff -r d404a6f6d01e6af5cbd35a427c474cee47fe963a -r 0e8235a516d16724fbe1ba2dababb18f4b53c6ef static/scripts/packed/mvc/upload/upload-ftp.js --- a/static/scripts/packed/mvc/upload/upload-ftp.js +++ b/static/scripts/packed/mvc/upload/upload-ftp.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());a.get({url:galaxy_config.root+"api/ftp_files",success:function(d){b._fill(d)}})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(c){if(c.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var b=0;for(key in c){this.add(c[key]);b+=c[key].size}this.$el.find("#upload-ftp-number").html(c.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(b,true))}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},add:function(f){var d=this;var e=$(this._templateRow(f));var b=e.find(".icon");$(this.el).find("tbody").append(e);var c="";if(this._find(f)){c=this.options.class_remove}else{c=this.options.class_add}b.addClass(c);e.on("click",function(){var g=d._find(f);b.removeClass();if(!g){d.app.uploadbox.add([{mode:"ftp",name:f.path,size:f.size,path:f.path}]);b.addClass(d.options.class_remove)}else{d.app.collection.remove(g);b.addClass(d.options.class_add)}})},_find:function(f){var c=this.app.collection.where({file_path:f.path});var b=null;for(var d in c){var e=c[d];if(e.get("status")=="init"&&e.get("file_mode")=="ftp"){b=e.get("id")}}return b},_templateRow:function(b){return'<tr class="upload-ftp-row" style="cursor: pointer;"><td><div class="icon"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+b.path+'</p></td><td style="white-space: nowrap;">'+a.bytesToString(b.size)+'</td><td style="white-space: nowrap;">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());a.get({url:galaxy_config.root+"api/ftp_files",success:function(d){b._fill(d)},error:function(){b._fill()}})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(c){if(c&&c.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var b=0;for(key in c){this.add(c[key]);b+=c[key].size}this.$el.find("#upload-ftp-number").html(c.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(b,true))}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},add:function(f){var d=this;var e=$(this._templateRow(f));var b=e.find(".icon");$(this.el).find("tbody").append(e);var c="";if(this._find(f)){c=this.options.class_remove}else{c=this.options.class_add}b.addClass(c);e.on("click",function(){var g=d._find(f);b.removeClass();if(!g){d.app.uploadbox.add([{mode:"ftp",name:f.path,size:f.size,path:f.path}]);b.addClass(d.options.class_remove)}else{d.app.collection.remove(g);b.addClass(d.options.class_add)}})},_find:function(f){var c=this.app.collection.where({file_path:f.path});var b=null;for(var d in c){var e=c[d];if(e.get("status")=="init"&&e.get("file_mode")=="ftp"){b=e.get("id")}}return b},_templateRow:function(b){return'<tr class="upload-ftp-row" style="cursor: pointer;"><td><div class="icon"/></td><td style="width: 200px"><p style="width: inherit; word-wrap: break-word;">'+b.path+'</p></td><td style="white-space: nowrap;">'+a.bytesToString(b.size)+'</td><td style="white-space: nowrap;">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Api: Ftp files return empty list instead of raising error if directory is missing
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d404a6f6d01e/ Changeset: d404a6f6d01e User: guerler Date: 2014-10-16 23:47:55+00:00 Summary: Api: Ftp files return empty list instead of raising error if directory is missing Affected #: 1 file diff -r eb28a9bcb4d9ca99613b667300095ce8a52f7ae3 -r d404a6f6d01e6af5cbd35a427c474cee47fe963a lib/galaxy/webapps/galaxy/api/ftp_files.py --- a/lib/galaxy/webapps/galaxy/api/ftp_files.py +++ b/lib/galaxy/webapps/galaxy/api/ftp_files.py @@ -112,8 +112,7 @@ response.append( dict( path = path, size = statinfo.st_size, ctime = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) - else: - raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' ) + # sort by path response = sorted(response, key=itemgetter("path")) return response 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: dannon: Tool's command might be separated by a newline, so we should use the general form split here, not specifically on spaces. Pointed out by @kellrott.
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb28a9bcb4d9/ Changeset: eb28a9bcb4d9 User: dannon Date: 2014-10-16 23:37:30+00:00 Summary: Tool's command might be separated by a newline, so we should use the general form split here, not specifically on spaces. Pointed out by @kellrott. Affected #: 1 file diff -r d09b44c5f22839e1b87f5673bdd1615b67b3ca51 -r eb28a9bcb4d9ca99613b667300095ce8a52f7ae3 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -699,7 +699,7 @@ def load_tooldir_tag_set(self, sub_elem, elems, tool_path, integrated_elems, load_panel_dict): directory = os.path.join( tool_path, sub_elem.attrib.get("dir") ) - recursive = string_as_bool( sub_elem.attrib.get("recursive", True) ) + recursive = string_as_bool( sub_elem.attrib.get("recursive", True) ) self.__watch_directory( directory, elems, integrated_elems, load_panel_dict, recursive ) def __watch_directory( self, directory, elems, integrated_elems, load_panel_dict, recursive): @@ -825,7 +825,7 @@ tool_tup = ( os.path.abspath( tool.config_file ), os.path.split( tool.config_file )[-1] ) tarball_files.append( tool_tup ) # TODO: This feels hacky. - tool_command = tool.command.strip().split( ' ' )[0] + tool_command = tool.command.strip().split()[0] tool_path = os.path.dirname( os.path.abspath( tool.config_file ) ) # Add the tool XML to the tuple that will be used to populate the tarball. if os.path.exists( os.path.join( tool_path, tool_command ) ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Fix Circster background bug in Firefox by correctly specifying colors.
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d09b44c5f228/ Changeset: d09b44c5f228 User: jgoecks Date: 2014-10-16 18:15:50+00:00 Summary: Fix Circster background bug in Firefox by correctly specifying colors. Affected #: 3 files diff -r 70c404e681a0f4c347eaca75d65f23a11edcb823 -r d09b44c5f22839e1b87f5673bdd1615b67b3ca51 client/galaxy/scripts/viz/circster.js --- a/client/galaxy/scripts/viz/circster.js +++ b/client/galaxy/scripts/viz/circster.js @@ -404,11 +404,11 @@ /* ----------------------- Public Methods ------------------------- */ initialize: function(options) { - this.bg_stroke = 'ddd'; + this.bg_stroke = '#ddd'; // Fill color when loading data. - this.loading_bg_fill = 'ffc'; + this.loading_bg_fill = '#ffc'; // Fill color when data has been loaded. - this.bg_fill = 'ddd'; + this.bg_fill = '#ddd'; this.total_gap = options.total_gap; this.track = options.track; this.radius_bounds = options.radius_bounds; @@ -688,8 +688,8 @@ // Use a single arc for rendering data. this.innerRadius = this.radius_bounds[0]; this.radius_bounds[0] = this.radius_bounds[1]; - this.bg_stroke = 'fff'; - this.bg_fill = 'fff'; + this.bg_stroke = '#fff'; + this.bg_fill = '#fff'; // Minimum arc distance for labels to be applied. this.min_arc_len = 0.05; diff -r 70c404e681a0f4c347eaca75d65f23a11edcb823 -r d09b44c5f22839e1b87f5673bdd1615b67b3ca51 static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -require(["utils/utils","libs/farbtastic",],function(a){a.cssLoadFile("static/style/circster.css")});define(["libs/underscore","libs/d3","viz/visualization","utils/config"],function(h,m,j,c){var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");return v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(Math.abs(p)<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));p=Math.abs(p);if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var d=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.genome=o.genome;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);var p=this.model.get("config");p.get("arc_dataset_height").on("change:value",this.update_track_bounds,this);p.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var q=this.get_circular_tracks(),s=this.model.get("config").get_value("arc_dataset_height"),r=this.model.get("config").get_value("track_gap"),o=Math.min(this.$el.width(),this.$el.height())-20,u=o/2-q.length*(s+r)+r-this.label_arc_height,t=m.range(u,o/2,s+r);var p=this;return h.map(t,function(v){return[v,v+s]})},render:function(){var x=this,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),r=this.get_chord_tracks(),q=x.model.get("config").get_value("total_gap"),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new e({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:q});y.render();return y});this.chords_views=r.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:q});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new d(),radius_bounds:u,genome:x.genome,total_gap:q});this.label_track_view.render()},add_track:function(u){var p=this.model.get("config").get_value("total_gap");if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:p});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new e({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:p});o.render();this.circular_views.push(o)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})},update_track_bounds:function(){var o=this.get_tracks_bounds();h.each(this.circular_views,function(p,q){p.update_radius_bounds(o[q])});h.each(this.chords_views,function(p){p.update_radius_bounds(o[0])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="ddd";this.loading_bg_fill="ffc";this.bg_fill="ddd";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(v){var u=h.reject(h.map(v,function(w,x){var y=null,z=q._get_path_function(r[x],w);if(z){y=z(w.data)}return y}),function(w){return w===null});var t=p.get("config").get_value("color");o.each(function(x,w){m.select(this).transition().duration(1000).style("stroke",t).style("fill",t).attr("d",u[w])})})}},_transition_labels:function(){},_update_data_bounds:function(p){var o=this.data_bounds;this.data_bounds=p||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));this._transition_chrom_data()},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);o.get("config").set_value("min_value",q.data_bounds[0],{silent:true});o.get("config").set_value("max_value",q.data_bounds[1],{silent:true});layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=2*Math.PI*this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var g=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);var p=this.track.get("config");p.get("min_value").on("change:value",this._update_min_max,this);p.get("max_value").on("change:value",this._update_min_max,this);p.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var p=this.track.get("config"),o=[p.get_value("min_value"),p.get_value("max_value")];this._update_data_bounds(o);this.parent_elt.selectAll(".min_max").text(function(r,q){return o[q]})},_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,q=function(){return"rotate(90)"};var p=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),q,true).classed("min_max",true);h.each(p,function(r){$(r).click(function(){var s=new c.ConfigSettingCollectionView({collection:o.track.get("config")});s.render_in_modal("Configure Track")})})},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(g.prototype,i);var e=g.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var f=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config);p.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset Height",type:"int",value:25,view:"circster"},{key:"track_gap",label:"Gap Between Tracks",type:"int",value:5,view:"circster"},{key:"total_gap",label:"Gap [0-1]",type:"float",value:0.4,view:"circster",hidden:true}]);var r=new a({el:$("#center .unified-panel-body"),genome:o,model:p});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"gear",title:"Settings",on_click:function(){var s=new c.ConfigSettingCollectionView({collection:p.get("config")});s.render_in_modal("Configure Visualization")}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:p.get("vis_id"),title:p.get("title"),dbkey:p.get("dbkey"),type:"trackster",vis_json:JSON.stringify(p)}}).success(function(s){Galaxy.modal.hide();p.set("vis_id",s.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:f}}); \ No newline at end of file +require(["utils/utils","libs/farbtastic",],function(a){a.cssLoadFile("static/style/circster.css")});define(["libs/underscore","libs/d3","viz/visualization","utils/config"],function(h,m,j,c){var n=Backbone.Model.extend({is_visible:function(r,o){var p=r.getBoundingClientRect(),q=$("svg")[0].getBoundingClientRect();if(p.right<0||p.left>q.right||p.bottom<0||p.top>q.bottom){return false}return true}});var i={drawTicks:function(s,r,w,q,o){var v=s.append("g").selectAll("g").data(r).enter().append("g").selectAll("g").data(w).enter().append("g").attr("class","tick").attr("transform",function(x){return"rotate("+(x.angle*180/Math.PI-90)+")translate("+x.radius+",0)"});var u=[],t=[],p=function(x){return x.angle>Math.PI?"end":null};if(o){u=[0,0,0,-4];t=[4,0,"",".35em"];p=null}else{u=[1,0,4,0];t=[0,4,".35em",""]}v.append("line").attr("x1",u[0]).attr("y1",u[1]).attr("x2",u[2]).attr("y1",u[3]).style("stroke","#000");return v.append("text").attr("x",t[0]).attr("y",t[1]).attr("dx",t[2]).attr("dy",t[3]).attr("text-anchor",p).attr("transform",q).text(function(x){return x.label})},formatNum:function(p,o){if(o===undefined){o=2}if(p===null){return null}var r=null;if(Math.abs(p)<1){r=p.toPrecision(o)}else{var q=Math.round(p.toPrecision(o));p=Math.abs(p);if(p<1000){r=q}else{if(p<1000000){r=Math.round((q/1000).toPrecision(3)).toFixed(0)+"K"}else{if(p<1000000000){r=Math.round((q/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return r}};var d=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(o){this.genome=o.genome;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("drawables").on("add",this.add_track,this);this.model.get("drawables").on("remove",this.remove_track,this);var p=this.model.get("config");p.get("arc_dataset_height").on("change:value",this.update_track_bounds,this);p.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(o){return o.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var q=this.get_circular_tracks(),s=this.model.get("config").get_value("arc_dataset_height"),r=this.model.get("config").get_value("track_gap"),o=Math.min(this.$el.width(),this.$el.height())-20,u=o/2-q.length*(s+r)+r-this.label_arc_height,t=m.range(u,o/2,s+r);var p=this;return h.map(t,function(v){return[v,v+s]})},render:function(){var x=this,o=x.$el.width(),w=x.$el.height(),t=this.get_circular_tracks(),r=this.get_chord_tracks(),q=x.model.get("config").get_value("total_gap"),s=this.get_tracks_bounds(),p=m.select(x.$el[0]).append("svg").attr("width",o).attr("height",w).attr("pointer-events","all").append("svg:g").call(m.behavior.zoom().on("zoom",function(){var y=m.event.scale;p.attr("transform","translate("+m.event.translate+") scale("+y+")");if(x.scale!==y){if(x.zoom_drag_timeout){clearTimeout(x.zoom_drag_timeout)}x.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+o/2+","+w/2+")").append("svg:g").attr("class","tracks");this.circular_views=t.map(function(z,A){var y=new e({el:p.append("g")[0],track:z,radius_bounds:s[A],genome:x.genome,total_gap:q});y.render();return y});this.chords_views=r.map(function(z){var y=new k({el:p.append("g")[0],track:z,radius_bounds:s[0],genome:x.genome,total_gap:q});y.render();return y});var v=this.circular_views[this.circular_views.length-1].radius_bounds[1],u=[v,v+this.label_arc_height];this.label_track_view=new b({el:p.append("g")[0],track:new d(),radius_bounds:u,genome:x.genome,total_gap:q});this.label_track_view.render()},add_track:function(u){var p=this.model.get("config").get_value("total_gap");if(u.get("track_type")==="DiagonalHeatmapTrack"){var q=this.circular_views[0].radius_bounds,t=new k({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:q,genome:this.genome,total_gap:p});t.render();this.chords_views.push(t)}else{var s=this.get_tracks_bounds();h.each(this.circular_views,function(v,w){v.update_radius_bounds(s[w])});h.each(this.chords_views,function(v){v.update_radius_bounds(s[0])});var r=this.circular_views.length,o=new e({el:m.select("g.tracks").append("g")[0],track:u,radius_bounds:s[r],genome:this.genome,total_gap:p});o.render();this.circular_views.push(o)}},remove_track:function(p,r,q){var o=this.circular_views[q.index];this.circular_views.splice(q.index,1);o.$el.remove();var s=this.get_tracks_bounds();h.each(this.circular_views,function(t,u){t.update_radius_bounds(s[u])})},update_track_bounds:function(){var o=this.get_tracks_bounds();h.each(this.circular_views,function(p,q){p.update_radius_bounds(o[q])});h.each(this.chords_views,function(p){p.update_radius_bounds(o[0])})}});var l=Backbone.View.extend({tagName:"g",initialize:function(o){this.bg_stroke="#ddd";this.loading_bg_fill="#ffc";this.bg_fill="#ddd";this.total_gap=o.total_gap;this.track=o.track;this.radius_bounds=o.radius_bounds;this.genome=o.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=m.select(this.$el[0])},get_fill_color:function(){var o=this.track.get("config").get_value("block_color");if(!o){o=this.track.get("config").get_value("color")}return o},render:function(){var s=this.parent_elt;var r=this.chroms_layout,u=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),o=s.selectAll("g").data(r).enter().append("svg:g"),q=o.append("path").attr("d",u).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);q.append("title").text(function(w){return w.data.chrom});var p=this,t=p.track.get("data_manager"),v=(t?t.data_is_ready():true);$.when(v).then(function(){$.when(p._render_data(s)).then(function(){q.style("fill",p.bg_fill);p.render_labels()})})},render_labels:function(){},update_radius_bounds:function(p){this.radius_bounds=p;var o=m.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",o);this._transition_chrom_data();this._transition_labels()},update_scale:function(r){var q=this.scale;this.scale=r;if(r<=q){return}var p=this,o=new n();this.parent_elt.selectAll("path.chrom-data").filter(function(t,s){return o.is_visible(this)}).each(function(y,u){var x=m.select(this),t=x.attr("chrom"),w=p.genome.get_chrom_region(t),v=p.track.get("data_manager"),s;if(!v.can_get_more_detailed_data(w)){return}s=p.track.get("data_manager").get_more_detailed_data(w,"Coverage",0,r);$.when(s).then(function(B){x.remove();p._update_data_bounds();var A=h.find(p.chroms_layout,function(C){return C.data.chrom===t});var z=p.get_fill_color();p._render_chrom_data(p.parent_elt,A,B).style("stroke",z).style("fill",z)})});return p},_transition_chrom_data:function(){var p=this.track,r=this.chroms_layout,o=this.parent_elt.selectAll("g>path.chrom-data"),s=o[0].length;if(s>0){var q=this;$.when(p.get("data_manager").get_genome_wide_data(this.genome)).then(function(v){var u=h.reject(h.map(v,function(w,x){var y=null,z=q._get_path_function(r[x],w);if(z){y=z(w.data)}return y}),function(w){return w===null});var t=p.get("config").get_value("color");o.each(function(x,w){m.select(this).transition().duration(1000).style("stroke",t).style("fill",t).attr("d",u[w])})})}},_transition_labels:function(){},_update_data_bounds:function(p){var o=this.data_bounds;this.data_bounds=p||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));this._transition_chrom_data()},_render_data:function(r){var q=this,p=this.chroms_layout,o=this.track,s=$.Deferred();$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(u){q.data_bounds=q.get_data_bounds(u);o.get("config").set_value("min_value",q.data_bounds[0],{silent:true});o.get("config").set_value("max_value",q.data_bounds[1],{silent:true});layout_and_data=h.zip(p,u),chroms_data_layout=h.map(layout_and_data,function(v){var w=v[0],x=v[1];return q._render_chrom_data(r,w,x)});var t=q.get_fill_color();q.parent_elt.selectAll("path.chrom-data").style("stroke",t).style("fill",t);s.resolve(r)});return s},_render_chrom_data:function(o,p,q){},_get_path_function:function(p,o){},_chroms_layout:function(){var p=this.genome.get_chroms_info(),r=m.layout.pie().value(function(t){return t.len}).sort(null),s=r(p),o=2*Math.PI*this.total_gap/p.length,q=h.map(s,function(v,u){var t=v.endAngle-o;v.endAngle=(t>v.startAngle?t:v.startAngle);return v});return q}});var b=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="#fff";this.bg_fill="#fff";this.min_arc_len=0.05},_render_data:function(q){var p=this,o=q.selectAll("g");o.selectAll("path").attr("id",function(u){return"label-"+u.data.chrom});o.append("svg:text").filter(function(u){return u.endAngle-u.startAngle>p.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(u){return"#label-"+u.data.chrom}).attr("startOffset","25%").text(function(u){return u.data.chrom});var r=function(w){var u=(w.endAngle-w.startAngle)/w.value,v=m.range(0,w.value,25000000).map(function(x,y){return{radius:p.innerRadius,angle:x*u+w.startAngle,label:y===0?0:(y%3?null:p.formatNum(x))}});if(v.length<4){v[v.length-1].label=p.formatNum(Math.round((v[v.length-1].angle-w.startAngle)/u))}return v};var t=function(u){return u.angle>Math.PI?"rotate(180)translate(-16)":null};var s=h.filter(this.chroms_layout,function(u){return u.endAngle-u.startAngle>p.min_arc_len});this.drawTicks(this.parent_elt,s,r,t)}});h.extend(b.prototype,i);var g=l.extend({initialize:function(o){l.prototype.initialize.call(this,o);var p=this.track.get("config");p.get("min_value").on("change:value",this._update_min_max,this);p.get("max_value").on("change:value",this._update_min_max,this);p.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var p=this.track.get("config"),o=[p.get_value("min_value"),p.get_value("max_value")];this._update_data_bounds(o);this.parent_elt.selectAll(".min_max").text(function(r,q){return o[q]})},_quantile:function(p,o){p.sort(m.ascending);return m.quantile(p,o)},_render_chrom_data:function(o,r,p){var s=this._get_path_function(r,p);if(!s){return null}var q=o.datum(p.data),t=q.append("path").attr("class","chrom-data").attr("chrom",r.data.chrom).attr("d",s);return t},_get_path_function:function(r,q){if(typeof q==="string"||!q.data||q.data.length===0){return null}var o=m.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var s=m.scale.linear().domain([0,q.data.length]).range([r.startAngle,r.endAngle]);var p=m.svg.line.radial().interpolate("linear").radius(function(t){return o(t[1])}).angle(function(u,t){return s(t)});return m.svg.area.radial().interpolate(p.interpolate()).innerRadius(o(0)).outerRadius(p.radius()).angle(p.angle())},render_labels:function(){var o=this,q=function(){return"rotate(90)"};var p=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),q,true).classed("min_max",true);h.each(p,function(r){$(r).click(function(){var s=new c.ConfigSettingCollectionView({collection:o.track.get("config")});s.render_in_modal("Configure Track")})})},_transition_labels:function(){if(this.data_bounds.length===0){return}var p=this,r=h.filter(this.chroms_layout,function(s){return s.endAngle-s.startAngle>0.08}),q=h.filter(r,function(t,s){return s%3===0}),o=h.flatten(h.map(q,function(s){return p._data_bounds_ticks_fn()(s)}));this.parent_elt.selectAll("g.tick").data(o).transition().attr("transform",function(s){return"rotate("+(s.angle*180/Math.PI-90)+")translate("+s.radius+",0)"})},_data_bounds_ticks_fn:function(){var o=this;visibleChroms=0;return function(p){return[{radius:o.radius_bounds[0],angle:p.startAngle,label:o.formatNum(o.data_bounds[0])},{radius:o.radius_bounds[1],angle:p.startAngle,label:o.formatNum(o.data_bounds[1])}]}},get_data_bounds:function(o){}});h.extend(g.prototype,i);var e=g.extend({get_data_bounds:function(p){var o=h.flatten(h.map(p,function(q){if(q){return h.map(q.data,function(r){return parseInt(r[1],10)||0})}else{return 0}}));return[h.min(o),this._quantile(o,0.98)||h.max(o)]}});var k=l.extend({render:function(){var o=this;$.when(o.track.get("data_manager").data_is_ready()).then(function(){$.when(o.track.get("data_manager").get_genome_wide_data(o.genome)).then(function(r){var q=[],p=o.genome.get_chroms_info();h.each(r,function(v,u){var s=p[u].chrom;var t=h.map(v.data,function(x){var w=o._get_region_angle(s,x[1]),y=o._get_region_angle(x[3],x[4]);return{source:{startAngle:w,endAngle:w+0.01},target:{startAngle:y,endAngle:y+0.01}}});q=q.concat(t)});o.parent_elt.append("g").attr("class","chord").selectAll("path").data(q).enter().append("path").style("fill",o.get_fill_color()).attr("d",m.svg.chord().radius(o.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(o){this.radius_bounds=o;this.parent_elt.selectAll("path").transition().attr("d",m.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(q,o){var p=h.find(this.chroms_layout,function(r){return r.data.chrom===q});return p.endAngle-((p.endAngle-p.startAngle)*(p.data.len-o)/p.data.len)}});var f=Backbone.View.extend({initialize:function(){var o=new j.Genome(galaxy_config.app.genome),p=new j.GenomeVisualization(galaxy_config.app.viz_config);p.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset Height",type:"int",value:25,view:"circster"},{key:"track_gap",label:"Gap Between Tracks",type:"int",value:5,view:"circster"},{key:"total_gap",label:"Gap [0-1]",type:"float",value:0.4,view:"circster",hidden:true}]);var r=new a({el:$("#center .unified-panel-body"),genome:o,model:p});r.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var q=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){j.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",p.get("dbkey"),function(s){p.add_tracks(s)})}},{icon_class:"gear",title:"Settings",on_click:function(){var s=new c.ConfigSettingCollectionView({collection:p.get("config")});s.render_in_modal("Configure Visualization")}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:p.get("vis_id"),title:p.get("title"),dbkey:p.get("dbkey"),type:"trackster",vis_json:JSON.stringify(p)}}).success(function(s){Galaxy.modal.hide();p.set("vis_id",s.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});q.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(q.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:f}}); \ No newline at end of file diff -r 70c404e681a0f4c347eaca75d65f23a11edcb823 -r d09b44c5f22839e1b87f5673bdd1615b67b3ca51 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -404,11 +404,11 @@ /* ----------------------- Public Methods ------------------------- */ initialize: function(options) { - this.bg_stroke = 'ddd'; + this.bg_stroke = '#ddd'; // Fill color when loading data. - this.loading_bg_fill = 'ffc'; + this.loading_bg_fill = '#ffc'; // Fill color when data has been loaded. - this.bg_fill = 'ddd'; + this.bg_fill = '#ddd'; this.total_gap = options.total_gap; this.track = options.track; this.radius_bounds = options.radius_bounds; @@ -688,8 +688,8 @@ // Use a single arc for rendering data. this.innerRadius = this.radius_bounds[0]; this.radius_bounds[0] = this.radius_bounds[1]; - this.bg_stroke = 'fff'; - this.bg_fill = 'fff'; + this.bg_stroke = '#fff'; + this.bg_fill = '#fff'; // Minimum arc distance for labels to be applied. this.min_arc_len = 0.05; 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: dannon: S3ObjectStore will create the bucket for you when possible if it does not exist.
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/70c404e681a0/ Changeset: 70c404e681a0 User: dannon Date: 2014-10-16 17:54:46+00:00 Summary: S3ObjectStore will create the bucket for you when possible if it does not exist. Affected #: 1 file diff -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 -r 70c404e681a0f4c347eaca75d65f23a11edcb823 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -167,8 +167,12 @@ log.debug("Using cloud object store with bucket '%s'" % bucket.name) return bucket except S3ResponseError: - log.debug("Could not get bucket '%s', attempt %s/5" % (bucket_name, i + 1)) - time.sleep(2) + try: + log.debug("Bucket not found, creating s3 bucket with handle '%s'" % bucket_name) + self.conn.create_bucket(bucket_name) + except S3ResponseError: + log.exception("Could not get bucket '%s', attempt %s/5" % (bucket_name, i + 1)) + time.sleep(2) # All the attempts have been exhausted and connection was not established, # raise error raise S3ResponseError 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: 2 new changesets
by commits-noreply＠bitbucket.org 16 Oct '14

16 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/921aa1c775b5/ Changeset: 921aa1c775b5 User: dannon Date: 2014-10-16 17:41:10+00:00 Summary: Slightly better handling of s3 object store conf, allowing connection element to be optional Affected #: 1 file diff -r 9f5491972e72ee38e011d49e891303e47bca29d9 -r 921aa1c775b54911c149fe3c8a1dc9645945a83d lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -77,7 +77,11 @@ b_xml = config_xml.findall('bucket')[0] self.bucket = b_xml.get('name') self.use_rr = b_xml.get('use_reduced_redundancy', False) - cn_xml = config_xml.findall('connection')[0] + cn_xml = config_xml.findall('connection') + if not cn_xml: + cn_xml = {} + else: + cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) self.is_secure = cn_xml.get('is_secure', True) https://bitbucket.org/galaxy/galaxy-central/commits/b1d9b4f49abb/ Changeset: b1d9b4f49abb User: dannon Date: 2014-10-16 17:41:22+00:00 Summary: Merge. Affected #: 65 files diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/collection/collection-li.js --- a/client/galaxy/scripts/mvc/collection/collection-li.js +++ b/client/galaxy/scripts/mvc/collection/collection-li.js @@ -100,8 +100,6 @@ /** add the DCE class to the list item */ className : ListItemView.prototype.className + " dataset-collection-element", - /** jq fx speed for this view */ - fxSpeed : 'fast', /** set up */ initialize : function( attributes ){ diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/history/history-structure-view.js --- /dev/null +++ b/client/galaxy/scripts/mvc/history/history-structure-view.js @@ -0,0 +1,421 @@ +define([ + 'mvc/job/job-model', + 'mvc/job/job-li', + 'mvc/history/history-content-model', + 'mvc/history/job-dag', + 'mvc/base-mvc', + 'utils/localization', + 'libs/d3' +], function( JOB, JOB_LI, HISTORY_CONTENT, JobDAG, BASE_MVC, _l ){ +// ============================================================================ +/* TODO: +change component = this to something else + +*/ +// ============================================================================ +/** + * + */ +var HistoryStructureComponent = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ + + //logger : console, + + className : 'history-structure-component', + + initialize : function( attributes ){ + this.log( this + '(HistoryStructureComponent).initialize:', attributes ); + this.component = attributes.component; + + this._jobLiMap = {}; + this._createJobModels(); + + this.layout = this._createLayout( attributes.layoutOptions ); + }, + + _createJobModels : function(){ + var view = this; + view.component.eachVertex( function( vertex ){ + var jobJSON = vertex.data.job, + job = new JOB.Job( jobJSON ); + + // get the models of the outputs for this job from the history + var outputModels = _.map( job.get( 'outputs' ), function( output ){ + //note: output is { src: 'hda/dataset_collection', id: <some id> } + // job output doesn't *quite* match up to normal typeId + var type = output.src === 'hda'? 'dataset' : 'dataset_collection', + typeId = HISTORY_CONTENT.typeIdStr( type, output.id ); + return view.model.contents.get( typeId ); + }); + // set the collection (HistoryContents) for the job to that json (setting historyId for proper ajax urls) + job.outputCollection.reset( outputModels ); + job.outputCollection.historyId = view.model.id; + //this.debug( job.outputCollection ); + + // create the bbone view for the job (to be positioned later accrd. to the layout) and cache + var li = new JOB_LI.JobListItemView({ model: job }); + //var li = new JOB_LI.JobListItemView({ model: job }); + li.render( 0 ).$el.appendTo( view.$el ); + view._jobLiMap[ job.id ] = li; + view._setUpJobListeners( li ); + + }); + return view.jobs; + }, + + _setUpJobListeners : function( jobLi ){ + // update the layout during expansion and collapsing of job and output li's + jobLi.on( 'expanding expanded collapsing collapsed', this.render, this ); + jobLi.foldout.on( 'view:expanding view:expanded view:collapsing view:collapsed', this.render, this ); + }, + + layoutDefaults : { + paddingTop : 8, + paddingLeft : 20, + linkSpacing : 16, + jobHeight : 308, + jobWidthSpacing : 320, + linkAdjX : 4, + linkAdjY : 0 + }, + + _createLayout : function( options ){ + options = _.defaults( _.clone( options || {} ), this.layoutDefaults ); + var view = this, + vertices = _.values( view.component.vertices ), + layout = _.extend( options, { + nodeMap : {}, + links : [], + el : { width: 0, height: 0 }, + svg : { width: 0, height: 0, top: 0, left: 0 } + }); + + vertices.forEach( function( v, j ){ + var node = { name: v.name, x: 0, y: 0 }; + layout.nodeMap[ v.name ] = node; + }); + + view.component.edges( function( e ){ + var link = { + source: e.source, + target: e.target + }; + layout.links.push( link ); + }); + //this.debug( JSON.stringify( layout, null, ' ' ) ); + return layout; + }, + + _updateLayout : function(){ + var view = this, + layout = view.layout; + + layout.svg.height = layout.paddingTop + ( layout.linkSpacing * _.size( layout.nodeMap ) ); + layout.el.height = layout.svg.height + layout.jobHeight; + +//TODO:?? can't we just alter the component v and e's directly? + // layout the job views putting jobWidthSpacing btwn each + var x = layout.paddingLeft, + y = layout.svg.height; + _.each( layout.nodeMap, function( node, jobId ){ + //this.debug( node, jobId ); + node.x = x; + node.y = y; + x += layout.jobWidthSpacing; + }); + layout.el.width = layout.svg.width = Math.max( layout.el.width, x ); + + // layout the links - connecting each job by it's main coords (currently) +//TODO: somehow adjust the svg height based on the largest distance the longest connection needs + layout.links.forEach( function( link ){ + var source = layout.nodeMap[ link.source ], + target = layout.nodeMap[ link.target ]; + link.x1 = source.x + layout.linkAdjX; + link.y1 = source.y + layout.linkAdjY; + link.x2 = target.x + layout.linkAdjX; + link.y2 = target.y + layout.linkAdjY; + }); + //this.debug( JSON.stringify( layout, null, ' ' ) ); + return this.layout; + }, + + render : function( options ){ + this.debug( this + '.render:', options ); + var view = this; + + function _render(){ + view._updateLayout(); + // set up the display containers + view.$el + .width( view.layout.el.width ) + .height( view.layout.el.height ); + view.renderSVG(); + + // position the job views accrd. to the layout + view.component.eachVertex( function( v ){ +//TODO:? liMap needed - can't we attach to vertex? + var li = view._jobLiMap[ v.name ], + position = view.layout.nodeMap[ li.model.id ]; + //this.debug( position ); + li.$el.css({ top: position.y, left: position.x }); + }); + } +//TODO: hack - li's invisible in updateLayout without this delay + if( !this.$el.is( ':visible' ) ){ + _.delay( _render, 0 ); + } else { + _render(); + } + return this; + }, + + renderSVG : function(){ + var view = this, + layout = view.layout; + + var svg = d3.select( this.el ).select( 'svg' ); + if( svg.empty() ){ + svg = d3.select( this.el ).append( 'svg' ); + } + + svg + .attr( 'width', layout.svg.width ) + .attr( 'height', layout.svg.height ); + + function highlightConnect( d ){ + d3.select( this ).classed( 'highlighted', true ); + view._jobLiMap[ d.source ].$el.addClass( 'highlighted' ); + view._jobLiMap[ d.target ].$el.addClass( 'highlighted' ); + } + + function unhighlightConnect( d ){ + d3.select( this ).classed( 'highlighted', false ); + view._jobLiMap[ d.source ].$el.removeClass( 'highlighted' ); + view._jobLiMap[ d.target ].$el.removeClass( 'highlighted' ); + } + + var connections = svg.selectAll( '.connection' ) + .data( layout.links ); + + connections + .enter().append( 'path' ) + .attr( 'class', 'connection' ) + .attr( 'id', function( d ){ return d.source + '-' + d.target; }) + .on( 'mouseover', highlightConnect ) + .on( 'mouseout', unhighlightConnect ); + + connections + .attr( 'd', function( d ){ return view._connectionPath( d ); }); + +//TODO: ? can we use tick here to update the links? + + return svg.node(); + }, + + _connectionPath : function( d ){ + var CURVE_X = 0, + controlY = ( ( d.x2 - d.x1 ) / this.layout.svg.width ) * this.layout.svg.height; + return [ + 'M', d.x1, ',', d.y1, ' ', + 'C', + d.x1 + CURVE_X, ',', d.y1 - controlY, ' ', + d.x2 - CURVE_X, ',', d.y2 - controlY, ' ', + d.x2, ',', d.y2 + ].join( '' ); + }, + + events : { + 'mouseover .job.list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, true ); }, + 'mouseout .job.list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, false ); } + }, + + highlightConnected : function( jobElement, highlight ){ + highlight = highlight !== undefined? highlight : true; + + var view = this, + component = view.component, + jobClassFn = highlight? jQuery.prototype.addClass : jQuery.prototype.removeClass, + connectionClass = highlight? 'connection highlighted' : 'connection'; + + //console.debug( 'mouseover', this ); + var $jobs = jobClassFn.call( $( jobElement ), 'highlighted' ), + id = $jobs.attr( 'id' ).replace( 'job-', '' ); + + // immed. ancestors + component.edges({ target: id }).forEach( function( edge ){ + jobClassFn.call( view.$( '#job-' + edge.source ), 'highlighted' ); + view.$( '#' + edge.source + '-' + id ).attr( 'class', connectionClass ); + }); + // descendants + component.vertices[ id ].eachEdge( function( edge ){ + jobClassFn.call( view.$( '#job-' + edge.target ), 'highlighted' ); + view.$( '#' + id + '-' + edge.target ).attr( 'class', connectionClass ); + }); + }, + + toString : function(){ + return 'HistoryStructureComponent(' + this.model.id + ')'; + } +}); + + +// ============================================================================ +/** + * + */ +var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({ + + //logger : console, + + className : HistoryStructureComponent.prototype.className + ' vertical', + + layoutDefaults : { + paddingTop : 8, + paddingLeft : 20, + linkSpacing : 16, + jobWidth : 308, + jobHeight : 308, + initialSpacing : 64, + jobSpacing : 16, + linkAdjX : 0, + linkAdjY : 4 + }, + +//TODO: how can we use the dom height of the job li's - they're not visible when this is called? + _updateLayout : function(){ + var view = this, + layout = view.layout; + //this.info( this.cid, '_updateLayout' ) + + layout.svg.width = layout.paddingLeft + ( layout.linkSpacing * _.size( layout.nodeMap ) ); + layout.el.width = layout.svg.width + layout.jobWidth; + + // reset height - we'll get the max Y below to assign to it + layout.el.height = 0; + +//TODO:?? can't we just alter the component v and e's directly? + var x = layout.svg.width, + y = layout.paddingTop; + _.each( layout.nodeMap, function( node, jobId ){ + //this.debug( node, jobId ); + node.x = x; + node.y = y; + var li = view._jobLiMap[ jobId ]; + if( li.$el.is( ':visible' ) ){ + y += li.$el.height() + layout.jobSpacing; + } else { + y += layout.initialSpacing + layout.jobSpacing; + } + }); + layout.el.height = layout.svg.height = Math.max( layout.el.height, y ); + + // layout the links - connecting each job by it's main coords (currently) + layout.links.forEach( function( link ){ + var source = layout.nodeMap[ link.source ], + target = layout.nodeMap[ link.target ]; + link.x1 = source.x + layout.linkAdjX; + link.y1 = source.y + layout.linkAdjY; + link.x2 = target.x + layout.linkAdjX; + link.y2 = target.y + layout.linkAdjY; + view.debug( 'link:', link.x1, link.y1, link.x2, link.y2, link ); + }); + //this.debug( JSON.stringify( layout, null, ' ' ) ); + view.debug( 'el:', layout.el ); + view.debug( 'svg:', layout.svg ); + return layout; + }, + + _connectionPath : function( d ){ + var CURVE_Y = 0, + controlX = ( ( d.y2 - d.y1 ) / this.layout.svg.height ) * this.layout.svg.width; + return [ + 'M', d.x1, ',', d.y1, ' ', + 'C', + d.x1 - controlX, ',', d.y1 + CURVE_Y, ' ', + d.x2 - controlX, ',', d.y2 - CURVE_Y, ' ', + d.x2, ',', d.y2 + ].join( '' ); + }, + + toString : function(){ + return 'VerticalHistoryStructureComponent(' + this.model.id + ')'; + } +}); + + +// ============================================================================ +/** + * + */ +var HistoryStructureView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ + + //logger : console, + + className : 'history-structure', + + initialize : function( attributes ){ + this.log( this + '(HistoryStructureView).initialize:', attributes, this.model ); +//TODO: to model + this.jobs = attributes.jobs; + this._createDAG(); + }, + + _createDAG : function(){ + this.dag = new JobDAG({ + historyContents : this.model.contents.toJSON(), + jobs : this.jobs, + excludeSetMetadata : true, + excludeErroredJobs : true + }); +//window.dag = this.dag; + this.log( this + '.dag:', this.dag ); + + this._createComponents(); + }, + + _createComponents : function(){ + this.log( this + '._createComponents' ); + var structure = this; +//window.structure = structure; + + structure.componentViews = structure.dag.weakComponentGraphArray().map( function( componentGraph ){ + return structure._createComponent( componentGraph ); + }); + }, + + _createComponent : function( component ){ + this.log( this + '._createComponent:', component ); + //return new HistoryStructureComponent({ + return new VerticalHistoryStructureComponent({ + model : this.model, + component : component + }); + }, + + render : function( options ){ + this.log( this + '.render:', options ); + var structure = this; + + structure.$el.html([ + '<div class="controls"></div>', + '<div class="components"></div>' + ].join( '' )); + + structure.componentViews.forEach( function( component ){ + component.render().$el.appendTo( structure.$components() ); + }); + return structure; + }, + + $components : function(){ + return this.$( '.components' ); + }, + + toString : function(){ + return 'HistoryStructureView(' + ')'; + } +}); + + +// ============================================================================ + return HistoryStructureView; +}); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/history/job-dag.js --- /dev/null +++ b/client/galaxy/scripts/mvc/history/job-dag.js @@ -0,0 +1,219 @@ +define([ + 'utils/graph', + 'utils/add-logging' +],function( GRAPH, addLogging ){ +// ============================================================================ +var _super = GRAPH.Graph; +/** A Directed acyclic Graph built from a history's job data. + * Reads in job json, filters and process that json, and builds a graph + * using the connections between job inputs and outputs. + */ +var JobDAG = function( options ){ + var self = this; + //this.logger = console; + + // instance vars +//TODO: needed? + self._historyContentsMap = {}; + self.filters = []; + + self._idMap = {}; + self.noInputJobs = []; + self.noOutputJobs = []; + +//TODO: save these? + self.filteredSetMetadata = []; + self.filteredErroredJobs = []; + + _super.call( self, true, null, options ); +}; +JobDAG.prototype = new GRAPH.Graph(); +JobDAG.prototype.constructor = JobDAG; + +// add logging ability - turn off/on using the this.logger statement above +addLogging( JobDAG ); + +// ---------------------------------------------------------------------------- +/** process jobs, options, filters, and any history data, then create the graph */ +JobDAG.prototype.init = function _init( options ){ + options = options || {}; + _super.prototype.init.call( this, options ); + + var self = this, + historyContentsJSON = options.historyContents || []; + jobsJSON = options.jobs || []; + + historyContentsJSON.forEach( function( content, i ){ + self._historyContentsMap[ content.id ] = _.clone( content ); + }); + + self.options = _.defaults( _.omit( options, 'historyContents', 'jobs' ), { + excludeSetMetadata : false + }); + self.filters = self._initFilters(); + +//TODO: O( 3N ) + self.preprocessJobs( _.clone( jobsJSON ) ); + self.createGraph(); + + return self; +}; + +/** add job filters based on options */ +JobDAG.prototype._initFilters = function __initFilters(){ + var self = this, + filters = []; + + if( self.options.excludeSetMetadata ){ + self.filteredSetMetadata = []; + filters.push( function filterSetMetadata( jobData ){ + if( jobData.job.tool_id !== '__SET_METADATA__' ){ return true; } + self.filteredSetMetadata.push( jobData.job.id ); + return false; + }); + } + + if( self.options.excludeErroredJobs ){ + self.filteredErroredJobs = []; + filters.push( function filterErrored( jobData ){ + if( jobData.job.state !== 'error' ){ return true; } + self.filteredErroredJobs.push( jobData.job.id ); + return false; + }); + } + + // all outputs deleted + // all outputs hidden + + if( _.isArray( self.options.filters ) ){ + filters = filters.concat( self.options.filters ); + } + self.debug( 'filters len:', filters.length ); + return filters; +}; + +/** sort the jobs and cache any that pass all filters into _idMap by job.id */ +JobDAG.prototype.preprocessJobs = function _preprocessJobs( jobs ){ + this.info( 'processing jobs' ); + + var self = this; +//TODO:? sorting neccessary? + self.sort( jobs ).forEach( function( job, i ){ + var jobData = self.preprocessJob( job, i ); + if( jobData ){ + self._idMap[ job.id ] = jobData; + } + }); + return self; +}; + +/** sort the jobs based on update time */ +JobDAG.prototype.sort = function _sort( jobs ){ + function cmpCreate( a, b ){ + if( a.update_time > b.update_time ){ return 1; } + if( a.update_time < b.update_time ){ return -1; } + return 0; + } + return jobs.sort( cmpCreate ); +}; + +/** proces input/output, filter based on job data returning data if passing, null if not */ +JobDAG.prototype.preprocessJob = function _preprocessJob( job, index ){ + //this.info( 'preprocessJob', job, index ); + var self = this, + jobData = { index: index, job: job }; + + jobData.inputs = self.datasetMapToIdArray( job.inputs, function( dataset, nameInJob ){ + //TODO:? store output name in self._datasets[ output.id ] from creating job? + }); + if( jobData.inputs.length === 0 ){ + self.noInputJobs.push( job.id ); + } + jobData.outputs = self.datasetMapToIdArray( job.outputs, function( dataset, nameInJob ){ + + }); + if( jobData.outputs.length === 0 ){ + self.noOutputJobs.push( job.id ); + } + + //self.debug( JSON.stringify( jobData, null, ' ' ) ); + // apply filters after processing job allowing access to the additional data above in the filters + for( var i=0; i<self.filters.length; i++ ){ + if( !self.filters[i].call( self, jobData ) ){ + self.debug( 'job', job.id, ' has been filtered out by function:\n', self.filters[i] ); + return null; + } + } + + //self.info( 'preprocessJob returning', jobData ); + return jobData; +}; + +/** make verbose input/output lists more concise, sanity checking along the way + * processFn is called on each input/output and passed the dataset obj (id,src) and the input/output name. + */ +JobDAG.prototype.datasetMapToIdArray = function _datasetMapToIdArray( datasetMap, processFn ){ + var self = this; + return _.map( datasetMap, function( dataset, nameInJob ){ + if( !dataset.id ){ + throw new Error( 'No id on datasetMap: ', JSON.stringify( dataset ) ); + } + if( !dataset.src || dataset.src !== 'hda' ){ + throw new Error( 'Bad src on datasetMap: ', JSON.stringify( dataset ) ); + } + processFn.call( self, dataset, nameInJob ); + return dataset.id; + }); +}; + +/** Walk all the jobs (vertices), attempting to find connections + * between datasets used as both inputs and outputs (edges) + */ +JobDAG.prototype.createGraph = function _createGraph(){ + var self = this; + self.debug( 'connections:' ); + + _.each( self._idMap, function( sourceJobData, sourceJobId ){ + self.debug( '\t', sourceJobId, sourceJobData ); + self.createVertex( sourceJobId, sourceJobData ); + + sourceJobData.usedIn = []; + _.each( sourceJobData.outputs, function( outputDatasetId ){ +//TODO: O(n^2) + _.each( self._idMap, function( targetJobData, targetJobId ){ + if( targetJobData === sourceJobData ){ return; } + + if( targetJobData.inputs.indexOf( outputDatasetId ) !== -1 ){ + self.info( '\t\t\t found connection: ', sourceJobId, targetJobId ); + sourceJobData.usedIn.push({ job: targetJobId, output: outputDatasetId }); + + self.createVertex( targetJobId, targetJobData ); + + self.createEdge( sourceJobId, targetJobId, self.directed, { + dataset : outputDatasetId + }); + } + }); + }); + }); + self.debug( 'job data: ', JSON.stringify( self._idMap, null, ' ' ) ); + return self; +}; + +/** Override to re-sort (ugh) jobs in each component by update time */ +Graph.prototype.weakComponentGraphArray = function(){ + return this.weakComponents().map( function( component ){ +//TODO: this seems to belong above (in sort) - why isn't it preserved? + component.vertices.sort( function cmpCreate( a, b ){ + if( a.data.job.update_time > b.data.job.update_time ){ return 1; } + if( a.data.job.update_time < b.data.job.update_time ){ return -1; } + return 0; + }); + return new Graph( this.directed, component ); + }); +}; + + +// ============================================================================ + return JobDAG; +}); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/job/job-li.js --- /dev/null +++ b/client/galaxy/scripts/mvc/job/job-li.js @@ -0,0 +1,129 @@ +define([ + 'mvc/list/list-item', + 'mvc/dataset/dataset-list', + "mvc/base-mvc", + "utils/localization" +], function( LIST_ITEM, DATASET_LIST, BASE_MVC, _l ){ +//============================================================================== +var _super = LIST_ITEM.FoldoutListItemView; +/** @class A job view used from within a larger list of jobs. + * Each job itself is a foldout panel of history contents displaying the outputs of this job. + */ +var JobListItemView = _super.extend(/** @lends JobListItemView.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + + className : _super.prototype.className + " job", + id : function(){ + return [ 'job', this.model.get( 'id' ) ].join( '-' ); + }, + + foldoutPanelClass : DATASET_LIST.DatasetList, + + /** Set up: instance vars, options, and event handlers */ + initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } + this.log( this + '.initialize:', attributes ); + _super.prototype.initialize.call( this, attributes ); + + /** where should pages from links be displayed? (default to new tab/window) */ + this.linkTarget = attributes.linkTarget || '_blank'; + }, + + /** In this override, add the state as a class for use with state-based CSS */ + _swapNewRender : function( $newRender ){ + _super.prototype._swapNewRender.call( this, $newRender ); + if( this.model.has( 'state' ) ){ + this.$el.addClass( 'state-' + this.model.get( 'state' ) ); + } + return this.$el; + }, + + /** Stub to return proper foldout panel options */ + _getFoldoutPanelOptions : function(){ + var options = _super.prototype._getFoldoutPanelOptions.call( this ); + return _.extend( options, { + collection : this.model.outputCollection, + selecting : false + }); + }, + + // ........................................................................ misc + /** String representation */ + toString : function(){ + return 'JobListItemView(' + this.model + ')'; + } +}); + +// ............................................................................ TEMPLATES +/** underscore templates */ +JobListItemView.prototype.templates = (function(){ +//TODO: move to require text! plugin + + var elTemplate = BASE_MVC.wrapTemplate([ + '<div class="list-element">', + '<div class="id"><%= model.id %></div>', + // errors, messages, etc. + '<div class="warnings"></div>', + + // multi-select checkbox + '<div class="selector">', + '<span class="fa fa-2x fa-square-o"></span>', + '</div>', + // space for title bar buttons - gen. floated to the right + '<div class="primary-actions"></div>', + '<div class="title-bar"></div>', + + // expandable area for more details + '<div class="details"></div>', + '</div>' + ]); + + var titleBarTemplate = BASE_MVC.wrapTemplate([ + // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display + '<div class="title-bar clear" tabindex="0">', + //'<span class="state-icon"></span>', + '<div class="title">', + '<span class="name"><%- job.tool_id %></span>', + '</div>', + '<div class="subtitle"></div>', + '</div>' + ], 'job' ); + + //var subtitleTemplate = BASE_MVC.wrapTemplate([ + // // override this + // '<div class="subtitle">', + // _l( 'Created' ), ': <%= new Date( job.create_time ).toString() %>, ', + // _l( 'Updated' ), ': <%= new Date( job.update_time ).toString() %>', + // '</div>' + //], 'job' ); + // + //var detailsTemplate = BASE_MVC.wrapTemplate([ + // '<div class="details">', + // '<div class="params">', + // '<% _.each( job.params, function( param, paramName ){ %>', + // '<div class="param">', + // '<label class="prompt"><%= paramName %></label>', + // '<span class="value"><%= param %></span>', + // '</div>', + // '<% }) %>', + // '</div>', + // '</div>' + //], 'job' ); + + return _.extend( {}, _super.prototype.templates, { + //el : elTemplate, + titleBar : titleBarTemplate, + //subtitle : subtitleTemplate, + //details : detailsTemplate + }); +}()); + + +//============================================================================= + return { + JobListItemView : JobListItemView + }; +}); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/job/job-model.js --- /dev/null +++ b/client/galaxy/scripts/mvc/job/job-model.js @@ -0,0 +1,203 @@ +define([ + "mvc/history/history-contents", + "mvc/dataset/states", + "utils/ajax-queue", + "mvc/base-mvc", + "utils/localization" +], function( HISTORY_CONTENTS, STATES, AJAX_QUEUE, BASE_MVC, _l ){ +//============================================================================== +var searchableMixin = BASE_MVC.SearchableModelMixin; +/** @class Represents a job running or ran on the server job handlers. + */ +var Job = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( + BASE_MVC.mixin( searchableMixin, /** @lends Job.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** default attributes for a model */ + defaults : { + model_class : 'Job', + + tool : null, + exit_code : null, + + inputs : {}, + outputs : {}, + params : {}, + + create_time : null, + update_time : null, + state : STATES.NEW + }, + + /** instance vars and listeners */ + initialize : function( attributes, options ){ + this.debug( this + '(Job).initialize', attributes, options ); + this.outputCollection = attributes.outputCollection || new HISTORY_CONTENTS.HistoryContents([]); + this._setUpListeners(); + }, + + /** set up any event listeners + * event: state:ready fired when this DA moves into/is already in a ready state + */ + _setUpListeners : function(){ + // if the state has changed and the new state is a ready state, fire an event + this.on( 'change:state', function( currModel, newState ){ + this.log( this + ' has changed state:', currModel, newState ); + if( this.inReadyState() ){ + this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); + } + }); + }, + + // ........................................................................ common queries + /** Is this job in a 'ready' state; where 'Ready' states are states where no + * processing is left to do on the server. + */ + inReadyState : function(){ + return _.contains( STATES.READY_STATES, this.get( 'state' ) ); + }, + + /** Does this model already contain detailed data (as opposed to just summary level data)? */ + hasDetails : function(){ + //?? this may not be reliable + return _.isEmpty( this.get( 'outputs' ) ); + }, + + // ........................................................................ ajax + /** root api url */ + urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' )) + 'api/jobs', + //url : function(){ return this.urlRoot; }, + + // ........................................................................ searching + // see base-mvc, SearchableModelMixin + /** what attributes of an Job will be used in a text search */ + searchAttributes : [ + 'tool' + ], + + // ........................................................................ misc + /** String representation */ + toString : function(){ + return [ 'Job(', this.get( 'id' ), ':', this.get( 'tool_id' ), ')' ].join( '' ); + } +})); + + +//============================================================================== +/** @class Backbone collection for Jobs. + */ +var JobCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends JobCollection.prototype */{ + model : Job, + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** root api url */ + urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' )) + 'api/jobs', + url : function(){ return this.urlRoot; }, + + intialize : function( models, options ){ + console.debug( models, options ); + }, + + // ........................................................................ common queries + /** Get the ids of every item in this collection + * @returns array of encoded ids + */ + ids : function(){ + return this.map( function( item ){ return item.get( 'id' ); }); + }, + + /** Get jobs that are not ready + * @returns array of content models + */ + notReady : function(){ + return this.filter( function( job ){ + return !job.inReadyState(); + }); + }, + + /** return true if any jobs don't have details */ + haveDetails : function(){ + return this.all( function( job ){ return job.hasDetails(); }); + }, + + // ........................................................................ ajax + /** fetches all details for each job in the collection using a queue */ + queueDetailFetching : function(){ + var collection = this, + queue = new AJAX_QUEUE.AjaxQueue( this.map( function( job ){ + return function(){ + return job.fetch({ silent: true }); + }; + })); + queue.done( function(){ + collection.trigger( 'details-loaded' ); + }); + return queue; + }, + + //toDAG : function(){ + // return new JobDAG( this.toJSON() ); + //}, + + // ........................................................................ sorting/filtering + /** return a new collection of jobs whose attributes contain the substring matchesWhat */ + matches : function( matchesWhat ){ + return this.filter( function( job ){ + return job.matches( matchesWhat ); + }); + }, + + // ........................................................................ misc + /** override to get a correct/smarter merge when incoming data is partial */ + set : function( models, options ){ + // arrrrrrrrrrrrrrrrrg... + // (e.g. stupid backbone) + // w/o this partial models from the server will fill in missing data with model defaults + // and overwrite existing data on the client + // see Backbone.Collection.set and _prepareModel + var collection = this; + models = _.map( models, function( model ){ + if( !collection.get( model.id ) ){ return model; } + + // merge the models _BEFORE_ calling the superclass version + var merged = existing.toJSON(); + _.extend( merged, model ); + return merged; + }); + // now call superclass when the data is filled + Backbone.Collection.prototype.set.call( this, models, options ); + }, + + /** String representation. */ + toString : function(){ + return ([ 'JobCollection(', this.length, ')' ].join( '' )); + } + +//----------------------------------------------------------------------------- class vars +}, { + /** class level fn for fetching the job details for all jobs in a history */ + fromHistory : function( historyId ){ + console.debug( this ); + var Collection = this, + collection = new Collection([]); + collection.fetch({ data: { history_id: historyId }}) + .done( function(){ + window.queue = collection.queueDetailFetching(); + + }); + return collection; + } +}); + + +//============================================================================= + return { + Job : Job, + JobCollection : JobCollection + }; +}); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/list/list-item.js --- a/client/galaxy/scripts/mvc/list/list-item.js +++ b/client/galaxy/scripts/mvc/list/list-item.js @@ -16,8 +16,8 @@ initialize : function( attributes ){ /** are the details of this view expanded/shown or not? */ this.expanded = attributes.expanded || false; - //this.log( '\t expanded:', this.expanded ); - this.fxSpeed = attributes.fxSpeed || this.fxSpeed; + this.log( '\t expanded:', this.expanded ); + this.fxSpeed = attributes.fxSpeed !== undefined? attributes.fxSpeed : this.fxSpeed; }, // ........................................................................ render main @@ -70,7 +70,9 @@ /** empty out the current el, move the $newRender's children in */ _swapNewRender : function( $newRender ){ - return this.$el.empty().attr( 'class', this.className ).append( $newRender.children() ); + return this.$el.empty() + .attr( 'class', _.isFunction( this.className )? this.className(): this.className ) + .append( $newRender.children() ); }, /** set up js behaviors, event handlers for elements within the given container @@ -117,15 +119,8 @@ */ expand : function(){ var view = this; - return view._fetchModelDetails() - .always(function(){ - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - view.$details().slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); + return view._fetchModelDetails().always( function(){ + view._expand(); }); }, @@ -139,6 +134,24 @@ return jQuery.when(); }, + /** Inner fn called when expand (public) has fetched the details */ + _expand : function(){ + var view = this, + $newDetails = view._renderDetails(); + view.$details().replaceWith( $newDetails ); + // needs to be set after the above or the slide will not show + view.expanded = true; + view.$details().slideDown({ + duration : view.fxSpeed, + step: function(){ + view.trigger( 'expanding', view ); + }, + complete: function(){ + view.trigger( 'expanded', view ); + } + }); + }, + /** Hide the body/details of an HDA. * @fires collapsed when a body has been collapsed */ @@ -146,8 +159,14 @@ this.debug( this + '(ExpandableView).collapse' ); var view = this; view.expanded = false; - this.$details().slideUp( view.fxSpeed, function(){ - view.trigger( 'collapsed', view ); + this.$details().slideUp({ + duration : view.fxSpeed, + step: function(){ + view.trigger( 'collapsing', view ); + }, + complete: function(){ + view.trigger( 'collapsed', view ); + } }); } @@ -204,7 +223,7 @@ $newRender.children( '.warnings' ).replaceWith( this._renderWarnings() ); $newRender.children( '.title-bar' ).replaceWith( this._renderTitleBar() ); $newRender.children( '.primary-actions' ).append( this._renderPrimaryActions() ); - $newRender.find( '.title-bar .subtitle' ).replaceWith( this._renderSubtitle() ); + $newRender.find( '> .title-bar .subtitle' ).replaceWith( this._renderSubtitle() ); return $newRender; }, @@ -375,11 +394,13 @@ * disrespect attributes.expanded if drilldown */ initialize : function( attributes ){ - ListItemView.prototype.initialize.call( this, attributes ); //TODO: hackish if( this.foldoutStyle === 'drilldown' ){ this.expanded = false; } this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle; this.foldoutPanelClass = attributes.foldoutPanelClass || this.foldoutPanelClass; + + ListItemView.prototype.initialize.call( this, attributes ); + this.foldout = this._createFoldoutPanel(); }, //TODO:?? override to exclude foldout scope? @@ -393,7 +414,7 @@ //TODO: hackish if( this.foldoutStyle === 'drilldown' ){ return $(); } var $newDetails = ListItemView.prototype._renderDetails.call( this ); - return this._attachFoldout( this._createFoldoutPanel(), $newDetails ); + return this._attachFoldout( this.foldout, $newDetails ); }, /** In this override, handle collection expansion. */ @@ -417,7 +438,8 @@ _getFoldoutPanelOptions : function(){ return { // propagate foldout style down - foldoutStyle : this.foldoutStyle + foldoutStyle : this.foldoutStyle, + fxSpeed : this.fxSpeed }; }, @@ -436,25 +458,13 @@ return view._fetchModelDetails() .always(function(){ if( view.foldoutStyle === 'foldout' ){ - view._expandByFoldout(); + view._expand(); } else if( view.foldoutStyle === 'drilldown' ){ view._expandByDrilldown(); } }); }, - /** For foldout, call render details then slide down */ - _expandByFoldout : function(){ - var view = this; - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - view.$details().slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); - }, - /** For drilldown, set up close handler and fire expanded:drilldown * containing views can listen to this and handle other things * (like hiding themselves) by listening for expanded/collapsed:drilldown @@ -462,7 +472,6 @@ _expandByDrilldown : function(){ var view = this; // attachment and rendering done by listener - view.foldout = this._createFoldoutPanel(); view.foldout.on( 'close', function(){ view.trigger( 'collapsed:drilldown', view, view.foldout ); }); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-content.js --- a/client/galaxy/scripts/mvc/tools/tools-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-content.js @@ -22,11 +22,16 @@ // get history summary Utils.get({ - url : self.base_url + '?deleted=false', + url : self.base_url + '?deleted=false&state=ok', success : function(response) { // backup summary self.summary = response; + // sort by id + self.summary.sort(function(a, b) { + return a.hid > b.hid ? -1 : (a.hid < b.hid ? 1 : 0); + }); + // log console.debug('tools-content::initialize() - Completed.'); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -27,10 +27,8 @@ this.modal = new Ui.Modal.View(); } - // link model/inputs and all options - this.options = options; - this.model = options.model; - this.inputs = options.model.inputs; + // link options + this.options = options; // set element this.setElement('<div/>'); @@ -53,9 +51,13 @@ // reset input element list, which contains the dom elements of each input element (includes also the input field) this.element_list = {}; - // initialize contents + // for now the initial tool model is parsed through the mako + this.model = this.options; + this.inputs = this.options.inputs; + + // request history content and build form this.content = new ToolContent({ - history_id : this.options.history_id, + history_id : self.options.history_id, success : function() { self._buildForm(); } @@ -89,6 +91,51 @@ console.debug('tools-form::refresh() - Recreated data structure. Refresh.'); }, + // build tool model through api call + _buildModel: function() { + // link this + var self = this; + + // construct url + var model_url = galaxy_config.root + 'api/tools/' + this.options.id + '/build?'; + if (this.options.job_id) { + model_url += 'job_id=' + this.options.job_id; + } else { + if (this.options.dataset_id) { + model_url += 'dataset_id=' + this.options.dataset_id; + } else { + var loc = top.location.href; + var pos = loc.indexOf('?'); + if (loc.indexOf('tool_id=') != -1 && pos !== -1) { + model_url += loc.slice(pos + 1); + } + } + } + + // get initial model + Utils.request({ + type : 'GET', + url : model_url, + success : function(response) { + // link model data update options + self.options = $.extend(self.options, response); + self.model = response; + self.inputs = response.inputs; + + // log success + console.debug('tools-form::initialize() - Initial tool model ready.'); + console.debug(response); + + // build form + self._buildForm(); + }, + error : function(response) { + console.debug('tools-form::initialize() - Initial tool model request failed.'); + console.debug(response); + } + }); + }, + // refresh form data _refreshForm: function() { // link this @@ -97,7 +144,7 @@ // finalize data var current_state = this.tree.finalize({ data : function(dict) { - if (dict.values.length > 0 && dict.values[0].src === 'hda') { + if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { return self.content.get({id: dict.values[0].id}).dataset_id; } return null; @@ -111,7 +158,7 @@ // post job Utils.request({ type : 'GET', - url : galaxy_config.root + 'tool_runner/index?tool_id=' + this.options.id + '&form_refresh=True', + url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', data : current_state, success : function(response) { console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); @@ -132,28 +179,31 @@ // button menu var menu = new Ui.ButtonMenu({ icon : 'fa-gear', - tooltip : 'Click to see a list of available operations.' + tooltip : 'Click to see a list of options.' }); - // add question option - menu.addMenu({ - icon : 'fa-question-circle', - title : 'Question?', - tooltip : 'Ask a question about this tool (Biostar)', - onclick : function() { - window.open(self.options.biostar_url + '/p/new/post/'); - } - }); - - // create search button - menu.addMenu({ - icon : 'fa-search', - title : 'Search', - tooltip : 'Search help for this tool (Biostar)', - onclick : function() { - window.open(self.options.biostar_url + '/t/' + self.options.id + '/'); - } - }); + // configure button selection + if(this.options.biostar_url) { + // add question option + menu.addMenu({ + icon : 'fa-question-circle', + title : 'Question?', + tooltip : 'Ask a question about this tool (Biostar)', + onclick : function() { + window.open(self.options.biostar_url + '/p/new/post/'); + } + }); + + // create search button + menu.addMenu({ + icon : 'fa-search', + title : 'Search', + tooltip : 'Search help for this tool (Biostar)', + onclick : function() { + window.open(self.options.biostar_url + '/t/' + self.options.id + '/'); + } + }); + }; // create share button menu.addMenu({ @@ -185,11 +235,11 @@ }); // switch to classic tool form mako if the form definition is incompatible - //if (this.incompatible) { + if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; - //} + } // create portlet this.portlet = new Portlet.View({ @@ -213,12 +263,6 @@ } }); - // configure button selection - if(!this.options.biostar_url) { - button_question.$el.hide(); - button_search.$el.hide(); - } - // append form this.$el.append(this.portlet.$el); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -37,7 +37,7 @@ console.debug(job_def); // show progress modal - this.app.modal.show({title: 'Please wait...', body: 'progress', buttons: { 'Close' : function () {self.app.modal.hide();} }}); + this.app.modal.show({title: 'Please wait...', body: 'progress', closing_events: true, buttons: { 'Close' : function () {self.app.modal.hide();} }}); // post job Utils.request({ @@ -55,10 +55,20 @@ var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { self._foundError(input_id, error_messages[input_id]); + break; } } else { // show error message with details console.debug(response); + self.app.modal.show({ + title : 'Job submission failed', + body : ToolTemplate.error(job_def), + buttons : { + 'Close' : function() { + self.app.modal.hide(); + } + } + }); } } }); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -529,22 +529,12 @@ /** Slider field */ _fieldSlider: function(input_def) { - // set min/max - input_def.min = input_def.min || 0; - input_def.max = input_def.max || 100000; - - // calculate step size - var step = 1; - if (input_def.type == 'float') { - step = (input_def.max - input_def.min) / 10000; - } - // create slider return new Ui.Slider.View({ id : 'field-' + input_def.id, + precise : input_def.type == 'float', min : input_def.min, - max : input_def.max, - step : step + max : input_def.max }); }, diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -40,7 +40,7 @@ var dataset_options = []; for (var i in datasets) { dataset_options.push({ - label: datasets[i].name, + label: datasets[i].hid + ': ' + datasets[i].name, value: datasets[i].id }); } @@ -67,7 +67,7 @@ var collection_options = []; for (var i in collections) { collection_options.push({ - label: collections[i].name, + label: collections[i].hid + ': ' + collections[i].name, value: collections[i].id }); } @@ -103,20 +103,36 @@ }, /** Return the currently selected dataset values */ - value : function () { - // identify select element - var select = null; - switch(this.current) { - case 'hda': - select = this.select_datasets; - break; - case 'hdca': - select = this.select_collection; - break; + value : function (dict) { + // update current value + if (dict !== undefined) { + try { + // set source + this.current = dict.values[0].src; + this.refresh(); + + // create list + var list = []; + for (var i in dict.values) { + list.push(dict.values[i].id); + } + + // identify select element + switch(this.current) { + case 'hda': + this.select_datasets.value(list); + break; + case 'hdca': + this.select_collection.value(list[0]); + break; + } + } catch (err) { + console.debug('tools-select-content::value() - Skipped.'); + } } // transform into an array - var id_list = select.value(); + var id_list = this._select().value(); if (!(id_list instanceof Array)) { id_list = [id_list]; } @@ -142,12 +158,7 @@ /** Validate current selection */ validate: function() { - switch(this.current) { - case 'hda': - return this.select_datasets.validate(); - case 'hdca': - return this.select_collection.validate(); - } + return this._select().validate(); }, /** Refreshes data selection view */ @@ -162,6 +173,16 @@ this.select_collection.$el.fadeIn(); break; } + }, + + /** Assists in selecting the current field */ + _select: function() { + switch(this.current) { + case 'hdca': + return this.select_collection; + default: + return this.select_datasets; + } } }); diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -49,7 +49,7 @@ error: function(job_def) { return '<div>' + '<p>' + - 'Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.' + + 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' + '</p>' + '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + JSON.stringify(job_def, undefined, 4) + diff -r 921aa1c775b54911c149fe3c8a1dc9645945a83d -r b1d9b4f49abb5f27bf54e01901fc37fe2fe20681 client/galaxy/scripts/mvc/ui/ui-slider.js --- a/client/galaxy/scripts/mvc/ui/ui-slider.js +++ b/client/galaxy/scripts/mvc/ui/ui-slider.js @@ -6,9 +6,11 @@ // options optionsDefault: { value : '', - min : 1, - max : 100, - step : 1 + min : null, + max : null, + step : null, + precise : false, + split : 10000 }, // initialize @@ -18,19 +20,35 @@ // configure options this.options = Utils.merge(options, this.optionsDefault); - + // create new element this.setElement(this._template(this.options)); - // backup slider - this.$slider = this.$el.find('#slider'); + // determine wether to use the slider + this.useslider = this.options.max !== null && this.options.min !== null && this.options.max > this.options.min; + + // set default step size + if (this.options.step === null) { + this.options.step = 1; + if (this.options.precise && this.useslider) { + this.options.step = (this.options.max - this.options.min) / this.options.split; + } + } + + // create slider if min and max are defined properly + if (this.useslider) { + this.$slider = this.$el.find('#slider'); + this.$slider.slider(this.options); + this.$slider.on('slide', function (event, ui) { + self.value(ui.value); + }); + } else { + this.$el.find('.ui-form-slider-text').css('width', '100%'); + } // backup integer field this.$text = this.$el.find('#text'); - // load slider plugin - this.$slider.slider(this.options); - // add text field event this.$text.on('change', function () { self.value($(this).val()); @@ -39,24 +57,23 @@ // add text field event this.$text.on('keydown', function (event) { var v = event.which; - console.log(v); if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || v == 189 || (v >= 48 && v <= 57) - || (self.options.step != 1 && $(this).val().indexOf('.') == -1) && v == 190)) { + || (self.options.precise && $(this).val().indexOf('.') == -1) && v == 190)) { event.preventDefault(); } }); - - // add slider event - this.$slider.on('slide', function (event, ui) { - self.value(ui.value); - }); }, // value value : function (new_val) { if (new_val !== undefined) { - // limit - new_val = Math.max(Math.min(new_val, this.options.max), this.options.min); + // apply limit + if (this.options.max !== null) { + new_val = Math.min(new_val, this.options.max); + } + if (this.options.min !== null) { + new_val = Math.max(new_val, this.options.min); + } // trigger on change event if (this.options.onchange) { @@ -64,7 +81,7 @@ } // set values - this.$slider.slider('value', new_val); + this.$slider && this.$slider.slider('value', new_val); this.$text.val(new_val); } This diff is so big that we needed to truncate the remainder. 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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