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

commit/galaxy-central: martenson: libraries: hidden buttons for creation of folders and libraries (no role checking implemented yet + no upload yet)
by commits-noreply＠bitbucket.org 26 Jan '14

26 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d658d4ec711d/ Changeset: d658d4ec711d User: martenson Date: 2014-01-26 19:25:49 Summary: libraries: hidden buttons for creation of folders and libraries (no role checking implemented yet + no upload yet) Affected #: 2 files diff -r 89a685c87b0ee5a04b36bb2e48c5b0fe00dd1e74 -r d658d4ec711d0c778b9ce07d700c3d3fee9aeca0 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -126,9 +126,8 @@ // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar" >'); - tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); + // tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); tmpl_array.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>'); - tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); @@ -809,14 +808,14 @@ tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); tmpl_array.push(''); tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); - tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); + // tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); tmpl_array.push('<table class="table table-condensed">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th class="button_heading"></th>'); tmpl_array.push(' <th>name</th>'); tmpl_array.push(' <th>description</th>'); tmpl_array.push(' <th>synopsis</th> '); - tmpl_array.push(' <th>model type</th> '); + // tmpl_array.push(' <th>model type</th> '); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); tmpl_array.push(' <% _.each(libraries, function(library) { %>'); @@ -826,7 +825,7 @@ tmpl_array.push(' <td><%- library.get("name") %></td>'); tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); + // tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% }); %>'); tmpl_array.push(' </tbody>'); diff -r 89a685c87b0ee5a04b36bb2e48c5b0fe00dd1e74 -r d658d4ec711d0c778b9ce07d700c3d3fee9aeca0 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(' <th class="button_heading">view</th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(" <td></td>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td></td>");r.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-folder-open"></span> browse</td>');r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(" <td>");r.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');r.push(' <span class="fa fa-eye"></span> details');r.push(" </button>");r.push(" </td>");r.push(' <td><%- content_item.get("name") %></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_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("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("/",{trigger:true,replace:false})}else{library_router.navigate("folders/"+r,{trigger:true,replace:false})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hide()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=Galaxy.modal;s.modal.show({closing_events:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hide()}}})},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hide();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hide();r.modal=null}}})},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hide();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return 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("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hide()}}})},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hide();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(' <th class="button_heading">view</th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(" <td></td>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td></td>");r.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-folder-open"></span> browse</td>');r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(" <td>");r.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');r.push(' <span class="fa fa-eye"></span> details');r.push(" </button>");r.push(" </td>");r.push(' <td><%- content_item.get("name") %></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_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("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("/",{trigger:true,replace:false})}else{library_router.navigate("folders/"+r,{trigger:true,replace:false})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hide()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. 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This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return 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("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hide()}}})},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hide();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ 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: greg: Fixes for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 26 Jan '14

26 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/89a685c87b0e/ Changeset: 89a685c87b0e User: greg Date: 2014-01-26 18:16:33 Summary: Fixes for the tool shed's install and test framework. Affected #: 3 files diff -r 196401191eb2556d92063fa5784eb57cd03aa5b1 -r 89a685c87b0ee5a04b36bb2e48c5b0fe00dd1e74 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -228,6 +228,11 @@ package_version, dependent_install_dir, tool_dependency_type='package' ) + if not can_install_tool_dependency: + log.debug( "Tool dependency %s version %s cannot be installed (it was probably previously installed), " % \ + ( str( tool_dependency.name, str( tool_dependency.version ) ) ) ) + log.debug( "so appending it to the list of handled tool dependencies." ) + handled_tool_dependencies.append( tool_dependency ) else: can_install_tool_dependency = True if can_install_tool_dependency: @@ -271,8 +276,6 @@ package_version=package_version, tool_dependencies_config=config_to_use ) suc.remove_file( tmp_filename ) - else: - handled_tool_dependencies.append( tool_dependency ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ ( str( required_repository_name ), str( required_repository_owner ), str( default_required_repository_changeset_revision ) ) @@ -345,6 +348,10 @@ package_version, install_dir, tool_dependency_type='package' ) + if not can_install_tool_dependency: + log.debug( "Tool dependency %s version %s cannot be installed (it was probably previously installed), so returning it." % \ + ( str( tool_dependency.name, str( tool_dependency.version ) ) ) ) + return tool_dependency else: can_install_tool_dependency = True if can_install_tool_dependency: diff -r 196401191eb2556d92063fa5784eb57cd03aa5b1 -r 89a685c87b0ee5a04b36bb2e48c5b0fe00dd1e74 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -26,6 +26,7 @@ relationships are defined in the repository_dependencies entry for each dictionary in the received list of repo_info_dicts. Each of these dictionaries is associated with a repository in the received tool_shed_repositories list. """ + log.debug( "Building repository dependency relationships..." ) for repo_info_dict in repo_info_dicts: for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ @@ -103,6 +104,7 @@ If the user elected to install repository dependencies, all items in the all_repo_info_dicts list will be processed. However, if repository dependencies are not to be installed, only those items contained in the received repo_info_dicts list will be processed. """ + log.debug( "Creating repository dependency objects..." ) # The following list will be maintained within this method to contain all created or updated tool shed repositories, including repository # dependencies that may not be installed. all_created_or_updated_tool_shed_repositories = [] @@ -140,8 +142,12 @@ trans.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, trans.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]: - log.debug( "Skipping installation of tool_shed_repository '%s' because it's installation status is '%s'." % \ - ( str( repository_db_record.name ), str( repository_db_record.status ) ) ) + debug_msg = "Skipping installation of revision %s of repository '%s' because it was installed " % \ + ( str( changeset_revision ), str( repository_db_record.name ) ) + debug_msg += "with the (possibly updated) revision %s and it's current installation status is '%s'." % \ + ( str( installed_changeset_revision ), str( repository_db_record.status ) ) + log.debug( debug_msg ) + can_update_db_record = False else: if repository_db_record.status in [ trans.install_model.ToolShedRepository.installation_status.ERROR, trans.install_model.ToolShedRepository.installation_status.NEW, diff -r 196401191eb2556d92063fa5784eb57cd03aa5b1 -r 89a685c87b0ee5a04b36bb2e48c5b0fe00dd1e74 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -43,7 +43,9 @@ return tool_dependencies def create_or_update_tool_dependency( app, tool_shed_repository, name, version, type, status, set_status=True ): - # Called from Galaxy (never the tool shed) when a new repository is being installed or when an uninstalled repository is being reinstalled. + """Create or update a tool_dependency record in the Galaxy database.""" + # Called from Galaxy (never the tool shed) when a new repository is being installed or when an uninstalled + # repository is being reinstalled. context = app.install_model.context # First see if an appropriate tool_dependency record exists for the received tool_shed_repository. if version: @@ -51,7 +53,8 @@ else: tool_dependency = get_tool_dependency_by_name_type_repository( app, tool_shed_repository, name, type ) if tool_dependency: - # In some cases we should not override the current status of an existing tool_dependency, so do so only if set_status is True. + # In some cases we should not override the current status of an existing tool_dependency, so do so only + # if set_status is True. if set_status: if str( tool_dependency.status ) != str( status ): debug_msg = 'Updating an existing record for version %s of tool dependency %s for revision %s of repository %s ' % \ @@ -584,7 +587,12 @@ # Shed's install and test framework is running. The Tool Shed's install and test framework which installs repositories # in 2 stages, those of type tool_dependency_definition followed by those containing valid tools and tool functional # test components. - sa_session = app.install_model.context.current + log.debug( "Synchronizing the database with the file system..." ) + try: + log.debug( "The value of app.config.running_functional_tests is: %s" % str( app.config.running_functional_tests ) ) + except: + pass + sa_session = app.install_model.context can_install_tool_dependency = False tool_dependency = get_tool_dependency_by_name_version_type_repository( app, tool_shed_repository, @@ -618,9 +626,9 @@ # tool dependencies are not deleted by default, from the "install and test" framework.. tool_dependency.status = app.install_model.ToolDependency.installation_status.INSTALLED else: - error_message = 'The installation directory for this tool dependency had contents, but the database had no record. ' + error_message = 'The installation directory for this tool dependency had contents but the database had no record. ' error_message += 'The installation log may show this tool dependency to be correctly installed, but due to the ' - error_message += 'missing database record, it is automatically set to Error.' + error_message += 'missing database record it is now being set to Error.' tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR tool_dependency.error_message = error_message else: @@ -637,6 +645,11 @@ can_install_tool_dependency = True sa_session.add( tool_dependency ) sa_session.flush() + try: + log.debug( "Returning from sync_database_with_file_system with tool_dependency %s, can_install_tool_dependency %s." % \ + ( str( tool_dependency.name ), str( can_install_tool_dependency ) ) ) + except Exception, e: + log.debug( str( e ) ) return tool_dependency, can_install_tool_dependency def tool_dependency_is_orphan( type, name, version, tools ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for 12257:9b337a87d6ec.
by commits-noreply＠bitbucket.org 26 Jan '14

26 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/196401191eb2/ Changeset: 196401191eb2 User: greg Date: 2014-01-26 16:15:33 Summary: Fixes for 12257:9b337a87d6ec. Affected #: 3 files diff -r 51798d8a3c92a2290537f6dcfb8f93e6f1371509 -r 196401191eb2556d92063fa5784eb57cd03aa5b1 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -171,7 +171,7 @@ return text -def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository ): +def handle_complex_repository_dependency_for_package( app, elem, package_name, package_version, tool_shed_repository, from_install_manager=False ): """ Inspect the repository defined by a complex repository dependency definition and take certain steps to enable installation of the received package name and version to proceed. The received elem is the <repository> tag set which defines the complex @@ -202,21 +202,32 @@ tool_dependency_version=package_version ) # Define this dependent repository's tool dependency installation directory that will contain the env.sh file with a path to the # required repository's installed tool dependency package. - dependent_install_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, - repository_name=tool_shed_repository.name, - repository_owner=tool_shed_repository.owner, - repository_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dependency_type='package', - tool_dependency_name=package_name, - tool_dependency_version=package_version ) + dependent_install_dir = \ + tool_dependency_util.get_tool_dependency_install_dir( app=app, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dependency_type='package', + tool_dependency_name=package_name, + tool_dependency_version=package_version ) if os.path.exists( dependent_install_dir ): - # Notice that we'll throw away the following tool_dependency if it can be installed. - tool_dependency, can_install_tool_dependency = tool_dependency_util.sync_database_with_file_system( app, - tool_shed_repository, - package_name, - package_version, - dependent_install_dir, - tool_dependency_type='package' ) + # The install manager handles tool migration stages and the sync_database_with_file_system() method handles two + # scenarios: (1) where a Galaxy file system environment related to installed tool shed repositories and tool dependencies + # has somehow (over time )gotten out of sync with the Galaxy database tables associated with these installed items, and + # (2) the Tool Shed's install and test framework which installs repositories in 2 stages, those of type + # tool_dependency_definition followed by those containing valid tools and tool functional test components. Neither of + # these scenarios apply when the install manager is running. + if from_install_manager: + can_install_tool_dependency = True + else: + # Notice that we'll throw away the following tool_dependency if it can be installed. + tool_dependency, can_install_tool_dependency = \ + tool_dependency_util.sync_database_with_file_system( app, + tool_shed_repository, + package_name, + package_version, + dependent_install_dir, + tool_dependency_type='package' ) else: can_install_tool_dependency = True if can_install_tool_dependency: @@ -300,7 +311,8 @@ package_elem, package_name, package_version, - tool_shed_repository ) + tool_shed_repository, + from_install_manager=from_install_manager ) for rd_tool_dependency in rd_tool_dependencies: if rd_tool_dependency.status == app.install_model.ToolDependency.installation_status.ERROR: # We'll log the error here, but continue installing packages since some may not require this dependency. @@ -315,11 +327,17 @@ tool_dependency_type='package', tool_dependency_name=package_name, tool_dependency_version=package_version ) - can_install_tool_dependency = True if os.path.exists( install_dir ): - if not from_install_manager: + # The install manager handles tool migration stages and the sync_database_with_file_system() method handles two + # scenarios: (1) where a Galaxy file system environment related to installed tool shed repositories and tool dependencies + # has somehow (over time )gotten out of sync with the Galaxy database tables associated with these installed items, and + # (2) the Tool Shed's install and test framework which installs repositories in 2 stages, those of type + # tool_dependency_definition followed by those containing valid tools and tool functional test components. Neither of + # these scenarios apply when the install manager is running. + if from_install_manager: + can_install_tool_dependency = True + else: # Notice that we'll throw away the following tool_dependency if it can be installed. - print 'Calling sync_database_with_file_system 2' tool_dependency, can_install_tool_dependency = \ tool_dependency_util.sync_database_with_file_system( app, tool_shed_repository, diff -r 51798d8a3c92a2290537f6dcfb8f93e6f1371509 -r 196401191eb2556d92063fa5784eb57cd03aa5b1 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -471,10 +471,12 @@ tool_dependency = tool_dependencies[ index ] if tool_dependency.can_install: # The database record is currently in a state that allows us to install the package on the file system. + log.debug( 'Attempting to install tool dependency package %s version %s.' % ( str( package_name ), str( package_version ) ) ) try: dependencies_ignored = not app.toolbox.dependency_manager.uses_tool_shed_dependencies() if dependencies_ignored: - log.debug( "Skipping package %s because tool shed dependency resolver not enabled." % str( package_name ) ) + log.debug( "Skipping installation of tool dependency package %s because tool shed dependency resolver not enabled." % \ + str( package_name ) ) # Tool dependency resolves have been configured and they do not include the tool shed. Do not install package. if app.toolbox.dependency_manager.find_dep( package_name, package_version, type='package') != INDETERMINATE_DEPENDENCY: ## TODO: Do something here such as marking it installed or @@ -493,7 +495,7 @@ tool_dependencies=tool_dependencies, from_install_manager=from_install_manager ) except Exception, e: - error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) ) + error_message = "Error installing tool dependency package %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) ) log.exception( error_message ) if tool_dependency: # Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must diff -r 51798d8a3c92a2290537f6dcfb8f93e6f1371509 -r 196401191eb2556d92063fa5784eb57cd03aa5b1 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -581,7 +581,9 @@ """ # This method should be reached very rarely. It implies that either the Galaxy environment became corrupted (i.e., # the database records for installed tool dependencies is not synchronized with tool dependencies on disk) or the Tool - # Shed's install and test framework is running. + # Shed's install and test framework is running. The Tool Shed's install and test framework which installs repositories + # in 2 stages, those of type tool_dependency_definition followed by those containing valid tools and tool functional + # test components. sa_session = app.install_model.context.current can_install_tool_dependency = False tool_dependency = get_tool_dependency_by_name_version_type_repository( app, 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: 6 new changesets
by commits-noreply＠bitbucket.org 25 Jan '14

25 Jan '14

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11597a078e65/ Changeset: 11597a078e65 User: nsoranzo Date: 2014-01-22 14:41:09 Summary: Fix typo in method name. Affected #: 1 file diff -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 -r 11597a078e6505087064315567ad3357c2d40c56 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -586,7 +586,7 @@ return data @expose_api - def import_shared_worflow(self, trans, payload, **kwd): + def import_shared_workflow(self, trans, payload, **kwd): """ POST /api/workflows/import Import a workflow shared by other users. https://bitbucket.org/galaxy/galaxy-central/commits/c7e4de2d6ed8/ Changeset: c7e4de2d6ed8 User: nsoranzo Date: 2014-01-22 15:05:51 Summary: Remove unused imports. Affected #: 1 file diff -r 11597a078e6505087064315567ad3357c2d40c56 -r c7e4de2d6ed888204c78d1f950d63a75c13a3386 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -5,16 +5,12 @@ import operator import os import re -import urllib from gettext import gettext import pkg_resources pkg_resources.require("SQLAlchemy >= 0.4") from sqlalchemy import func, and_, select -pkg_resources.require( "Routes" ) -import routes - from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError from paste.httpexceptions import HTTPNotImplemented, HTTPRequestRangeNotSatisfiable from galaxy.exceptions import ItemAccessibilityException, ItemDeletionException, ItemOwnershipException @@ -40,7 +36,6 @@ from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation, HistoryDatasetAssociation -from galaxy.datatypes.display_applications import util as da_util from galaxy.datatypes.metadata import FileParameter https://bitbucket.org/galaxy/galaxy-central/commits/1f91923153d2/ Changeset: 1f91923153d2 User: nsoranzo Date: 2014-01-22 14:46:36 Summary: Move duplicated method _workflow_from_dict to UsesStoredWorkflowMixin. Affected #: 3 files diff -r c7e4de2d6ed888204c78d1f950d63a75c13a3386 -r 1f91923153d2d64a216ddbeb06810df3ac12be06 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -37,6 +37,7 @@ from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation, HistoryDatasetAssociation from galaxy.datatypes.metadata import FileParameter +from galaxy.util.json import to_json_string log = logging.getLogger( __name__ ) @@ -1554,6 +1555,102 @@ session.flush() return imported_stored + def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): + """ + Creates a workflow from a dict. Created workflow is stored in the database and returned. + """ + from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps + + # Put parameters in workflow mode + trans.workflow_building_mode = True + # Create new workflow from incoming dict + workflow = model.Workflow() + # If there's a source, put it in the workflow name. + if source: + name = "%s (imported from %s)" % ( data['name'], source ) + else: + name = data['name'] + workflow.name = name + # Assume no errors until we find a step that has some + workflow.has_errors = False + # Create each step + steps = [] + # The editor will provide ids for each step that we don't need to save, + # but do need to use to make connections + steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the local Galaxy instance. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] + # First pass to build step objects and populate basic values + for step_dict in data[ 'steps' ].itervalues(): + # Create the model class for the step + step = model.WorkflowStep() + steps.append( step ) + steps_by_external_id[ step_dict['id' ] ] = step + # FIXME: Position should be handled inside module + step.position = step_dict['position'] + module = module_factory.from_dict( trans, step_dict, secure=False ) + module.save_to_step( step ) + if module.type == 'tool' and module.tool is None: + # A required tool is not available in the local Galaxy instance. + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) + # Save the entire step_dict in the unused config field, be parsed later + # when we do have the tool + step.config = to_json_string(step_dict) + if step.tool_errors: + workflow.has_errors = True + # Stick this in the step temporarily + step.temp_input_connections = step_dict['input_connections'] + # Save step annotation. + annotation = step_dict[ 'annotation' ] + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) + # Second pass to deal with connections between steps + for step in steps: + # Input connections + for input_name, conn_list in step.temp_input_connections.iteritems(): + if not conn_list: + continue + if not isinstance(conn_list, list): # Older style singleton connection + conn_list = [conn_list] + for conn_dict in conn_list: + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_name = conn_dict['output_name'] + conn.output_step = steps_by_external_id[ conn_dict['id'] ] + del step.temp_input_connections + + # Order the steps if possible + attach_ordered_steps( workflow, steps ) + + # Connect up + stored = model.StoredWorkflow() + stored.name = workflow.name + workflow.stored_workflow = stored + stored.latest_workflow = workflow + stored.user = trans.user + if data[ 'annotation' ]: + self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) + + # Persist + trans.sa_session.add( stored ) + trans.sa_session.flush() + + if add_to_menu: + if trans.user.stored_workflow_menu_entries == None: + trans.user.stored_workflow_menu_entries = [] + menuEntry = model.StoredWorkflowMenuEntry() + menuEntry.stored_workflow = stored + trans.user.stored_workflow_menu_entries.append( menuEntry ) + trans.sa_session.flush() + + return stored, missing_tool_tups + class UsesFormDefinitionsMixin: """Mixin for controllers that use Galaxy form objects.""" diff -r c7e4de2d6ed888204c78d1f950d63a75c13a3386 -r 1f91923153d2d64a216ddbeb06810df3ac12be06 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -9,14 +9,12 @@ from galaxy import exceptions from galaxy import util from galaxy import web -from galaxy import model from galaxy.tools.parameters import visit_input_values, DataToolParameter, RuntimeValue from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.workflow.modules import module_factory, ToolModule from galaxy.jobs.actions.post import ActionBox -from ..controllers.workflow import attach_ordered_steps log = logging.getLogger(__name__) @@ -367,89 +365,6 @@ return item - def _workflow_from_dict( self, trans, data, source=None ): - """ - RPARK: copied from galaxy.webapps.galaxy.controllers.workflows.py - Creates a workflow from a dict. Created workflow is stored in the database and returned. - """ - # Put parameters in workflow mode - trans.workflow_building_mode = True - # Create new workflow from incoming dict - workflow = model.Workflow() - # If there's a source, put it in the workflow name. - if source: - name = "%s (imported from %s)" % ( data['name'], source ) - else: - name = data['name'] - workflow.name = name - # Assume no errors until we find a step that has some - workflow.has_errors = False - # Create each step - steps = [] - # The editor will provide ids for each step that we don't need to save, - # but do need to use to make connections - steps_by_external_id = {} - # Keep track of tools required by the workflow that are not available in - # the local Galaxy instance. Each tuple in the list of missing_tool_tups - # will be ( tool_id, tool_name, tool_version ). - missing_tool_tups = [] - # First pass to build step objects and populate basic values - for step_dict in data[ 'steps' ].itervalues(): - # Create the model class for the step - step = model.WorkflowStep() - steps.append( step ) - steps_by_external_id[ step_dict['id' ] ] = step - # FIXME: Position should be handled inside module - step.position = step_dict['position'] - module = module_factory.from_dict( trans, step_dict, secure=False ) - if module.type == 'tool' and module.tool is None: - # A required tool is not available in the local Galaxy instance. - missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) - if missing_tool_tup not in missing_tool_tups: - missing_tool_tups.append( missing_tool_tup ) - module.save_to_step( step ) - if step.tool_errors: - workflow.has_errors = True - # Stick this in the step temporarily - step.temp_input_connections = step_dict['input_connections'] - # Save step annotation. - #annotation = step_dict[ 'annotation' ] - #if annotation: - #annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - # ------------------------------------------ # - # RPARK REMOVING: user annotation b/c of API - #self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) - # ------------------------------------------ # - # Unpack and add post-job actions. - post_job_actions = step_dict.get( 'post_job_actions', {} ) - for name, pja_dict in post_job_actions.items(): - model.PostJobAction( pja_dict[ 'action_type' ], - step, pja_dict[ 'output_name' ], - pja_dict[ 'action_arguments' ] ) - # Second pass to deal with connections between steps - for step in steps: - # Input connections - for input_name, conn_dict in step.temp_input_connections.iteritems(): - if conn_dict: - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] - del step.temp_input_connections - # Order the steps if possible - attach_ordered_steps( workflow, steps ) - # Connect up - stored = model.StoredWorkflow() - stored.name = workflow.name - workflow.stored_workflow = stored - stored.latest_workflow = workflow - stored.user = trans.user - # Persist - trans.sa_session.add( stored ) - trans.sa_session.flush() - return stored, missing_tool_tups - def _workflow_to_dict( self, trans, stored ): """ RPARK: copied from galaxy.web.controllers.workflows.py diff -r c7e4de2d6ed888204c78d1f950d63a75c13a3386 -r 1f91923153d2d64a216ddbeb06810df3ac12be06 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -24,7 +24,6 @@ from galaxy.tools.parameters import RuntimeValue, visit_input_values from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue from galaxy.tools.parameters.grouping import Conditional, Repeat -from galaxy.util.json import to_json_string from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html from galaxy.util.topsort import CycleError, topsort, topsort_levels @@ -1734,100 +1733,6 @@ data['steps'][step.order_index] = step_dict return data - def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): - """ - Creates a workflow from a dict. Created workflow is stored in the database and returned. - """ - # Put parameters in workflow mode - trans.workflow_building_mode = True - # Create new workflow from incoming dict - workflow = model.Workflow() - # If there's a source, put it in the workflow name. - if source: - name = "%s (imported from %s)" % ( data['name'], source ) - else: - name = data['name'] - workflow.name = name - # Assume no errors until we find a step that has some - workflow.has_errors = False - # Create each step - steps = [] - # The editor will provide ids for each step that we don't need to save, - # but do need to use to make connections - steps_by_external_id = {} - # Keep track of tools required by the workflow that are not available in - # the local Galaxy instance. Each tuple in the list of missing_tool_tups - # will be ( tool_id, tool_name, tool_version ). - missing_tool_tups = [] - # First pass to build step objects and populate basic values - for key, step_dict in data[ 'steps' ].iteritems(): - # Create the model class for the step - step = model.WorkflowStep() - steps.append( step ) - steps_by_external_id[ step_dict['id' ] ] = step - # FIXME: Position should be handled inside module - step.position = step_dict['position'] - module = module_factory.from_dict( trans, step_dict, secure=False ) - module.save_to_step( step ) - if module.type == 'tool' and module.tool is None: - # A required tool is not available in the local Galaxy instance. - missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) - if missing_tool_tup not in missing_tool_tups: - missing_tool_tups.append( missing_tool_tup ) - # Save the entire step_dict in the unused config field, be parsed later - # when we do have the too when we do have the tool - step.config = to_json_string(step_dict) - if step.tool_errors: - workflow.has_errors = True - # Stick this in the step temporarily - step.temp_input_connections = step_dict['input_connections'] - # Save step annotation. - annotation = step_dict[ 'annotation' ] - if annotation: - annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) - # Second pass to deal with connections between steps - for step in steps: - # Input connections - for input_name, conn_list in step.temp_input_connections.iteritems(): - if not conn_list: - continue - if not isinstance(conn_list, list): # Older style singleton connection - conn_list = [conn_list] - for conn_dict in conn_list: - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] - del step.temp_input_connections - - # Order the steps if possible - attach_ordered_steps( workflow, steps ) - - # Connect up - stored = model.StoredWorkflow() - stored.name = workflow.name - workflow.stored_workflow = stored - stored.latest_workflow = workflow - stored.user = trans.user - if data[ 'annotation' ]: - self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) - - # Persist - trans.sa_session.add( stored ) - trans.sa_session.flush() - - if add_to_menu: - if trans.user.stored_workflow_menu_entries == None: - trans.user.stored_workflow_menu_entries = [] - menuEntry = model.StoredWorkflowMenuEntry() - menuEntry.stored_workflow = stored - trans.user.stored_workflow_menu_entries.append( menuEntry ) - trans.sa_session.flush() - - return stored, missing_tool_tups - def _workflow_to_svg_canvas( self, trans, stored ): workflow = stored.latest_workflow data = [] https://bitbucket.org/galaxy/galaxy-central/commits/7ed68c60b454/ Changeset: 7ed68c60b454 User: nsoranzo Date: 2014-01-22 15:50:09 Summary: Move duplicated method _workflow_to_dict to UsesStoredWorkflowMixin. Affected #: 3 files diff -r 1f91923153d2d64a216ddbeb06810df3ac12be06 -r 7ed68c60b4546c90f24f4463b644f6fffe712596 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -37,7 +37,10 @@ from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation, HistoryDatasetAssociation from galaxy.datatypes.metadata import FileParameter +from galaxy.tools.parameters import RuntimeValue, visit_input_values +from galaxy.tools.parameters.basic import DataToolParameter from galaxy.util.json import to_json_string +from galaxy.workflow.modules import ToolModule log = logging.getLogger( __name__ ) @@ -1651,6 +1654,131 @@ return stored, missing_tool_tups + def _workflow_to_dict( self, trans, stored ): + """ + Converts a workflow to a dict of attributes suitable for exporting. + """ + workflow = stored.latest_workflow + workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored ) + annotation_str = "" + if workflow_annotation: + annotation_str = workflow_annotation.annotation + # Pack workflow data into a dictionary and return + data = {} + data['a_galaxy_workflow'] = 'true' # Placeholder for identifying galaxy workflow + data['format-version'] = "0.1" + data['name'] = workflow.name + data['annotation'] = annotation_str + data['steps'] = {} + # For each step, rebuild the form and encode the state + for step in workflow.steps: + # Load from database representation + module = module_factory.from_workflow_step( trans, step ) + if not module: + return None + # Get user annotation. + step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) + annotation_str = "" + if step_annotation: + annotation_str = step_annotation.annotation + # Step info + step_dict = { + 'id': step.order_index, + 'type': module.type, + 'tool_id': module.get_tool_id(), + 'tool_version' : step.tool_version, + 'name': module.get_name(), + 'tool_state': module.get_state( secure=False ), + 'tool_errors': module.get_errors(), + ## 'data_inputs': module.get_data_inputs(), + ## 'data_outputs': module.get_data_outputs(), + 'annotation' : annotation_str + } + # Add post-job actions to step dict. + if module.type == 'tool': + pja_dict = {} + for pja in step.post_job_actions: + pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, + output_name = pja.output_name, + action_arguments = pja.action_arguments ) + step_dict[ 'post_job_actions' ] = pja_dict + # Data inputs + step_dict['inputs'] = [] + if module.type == "data_input": + # Get input dataset name; default to 'Input Dataset' + name = module.state.get( 'name', 'Input Dataset') + step_dict['inputs'].append( { "name" : name, "description" : annotation_str } ) + else: + # Step is a tool and may have runtime inputs. + for name, val in module.state.inputs.items(): + input_type = type( val ) + if input_type == RuntimeValue: + step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) + elif input_type == dict: + # Input type is described by a dict, e.g. indexed parameters. + for partval in val.values(): + if type( partval ) == RuntimeValue: + step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) + # User outputs + step_dict['user_outputs'] = [] + """ + module_outputs = module.get_data_outputs() + step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step ) + for output in step_outputs: + name = output.output_name + annotation = "" + for module_output in module_outputs: + if module_output.get( 'name', None ) == name: + output_type = module_output.get( 'extension', '' ) + break + data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type } + """ + + # All step outputs + step_dict['outputs'] = [] + if type( module ) is ToolModule: + for output in module.get_data_outputs(): + step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) + # Connections + input_connections = step.input_connections + if step.type is None or step.type == 'tool': + # Determine full (prefixed) names of valid input datasets + data_input_names = {} + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + data_input_names[ prefixed_name ] = True + + # FIXME: this updates modules silently right now; messages from updates should be provided. + module.check_and_update_state() + visit_input_values( module.tool.inputs, module.state.inputs, callback ) + # Filter + # FIXME: this removes connection without displaying a message currently! + input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] + # Encode input connections as dictionary + input_conn_dict = {} + unique_input_names = set( [conn.input_name for conn in input_connections] ) + for input_name in unique_input_names: + input_conn_dict[ input_name ] = \ + [ dict( id=conn.output_step.order_index, output_name=conn.output_name ) for conn in input_connections if conn.input_name == input_name ] + # Preserve backward compatability. Previously Galaxy + # assumed input connections would be dictionaries not + # lists of dictionaries, so replace any singleton list + # with just the dictionary so that workflows exported from + # newer Galaxy instances can be used with older Galaxy + # instances if they do no include multiple input + # tools. This should be removed at some point. Mirrored + # hack in _workflow_from_dict should never be removed so + # existing workflow exports continue to function. + for input_name, input_conn in dict(input_conn_dict).iteritems(): + if len(input_conn) == 1: + input_conn_dict[input_name] = input_conn[0] + step_dict['input_connections'] = input_conn_dict + # Position + step_dict['position'] = step.position + # Add to return value + data['steps'][step.order_index] = step_dict + return data + class UsesFormDefinitionsMixin: """Mixin for controllers that use Galaxy form objects.""" diff -r 1f91923153d2d64a216ddbeb06810df3ac12be06 -r 7ed68c60b4546c90f24f4463b644f6fffe712596 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -9,10 +9,10 @@ from galaxy import exceptions from galaxy import util from galaxy import web -from galaxy.tools.parameters import visit_input_values, DataToolParameter, RuntimeValue +from galaxy.tools.parameters import visit_input_values, DataToolParameter from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin -from galaxy.workflow.modules import module_factory, ToolModule +from galaxy.workflow.modules import module_factory from galaxy.jobs.actions.post import ActionBox @@ -365,141 +365,6 @@ return item - def _workflow_to_dict( self, trans, stored ): - """ - RPARK: copied from galaxy.web.controllers.workflows.py - Converts a workflow to a dict of attributes suitable for exporting. - """ - workflow = stored.latest_workflow - - ### ----------------------------------- ### - ## RPARK EDIT ## - workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored ) - annotation_str = "" - if workflow_annotation: - annotation_str = workflow_annotation.annotation - ### ----------------------------------- ### - - - # Pack workflow data into a dictionary and return - data = {} - data['a_galaxy_workflow'] = 'true' # Placeholder for identifying galaxy workflow - data['format-version'] = "0.1" - data['name'] = workflow.name - ### ----------------------------------- ### - ## RPARK EDIT ## - data['annotation'] = annotation_str - ### ----------------------------------- ### - - data['steps'] = {} - # For each step, rebuild the form and encode the state - for step in workflow.steps: - # Load from database representation - module = module_factory.from_workflow_step( trans, step ) - if not module: - return None - - ### ----------------------------------- ### - ## RPARK EDIT ## - - # TODO: This is duplicated from - # lib/galaxy/webapps/controllres/workflow.py -- refactor and - # eliminate copied code. - - # Get user annotation. - step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) - annotation_str = "" - if step_annotation: - annotation_str = step_annotation.annotation - ### ----------------------------------- ### - - # Step info - step_dict = { - 'id': step.order_index, - 'type': module.type, - 'tool_id': module.get_tool_id(), - 'tool_version' : step.tool_version, - 'name': module.get_name(), - 'tool_state': module.get_state( secure=False ), - 'tool_errors': module.get_errors(), - ## 'data_inputs': module.get_data_inputs(), - ## 'data_outputs': module.get_data_outputs(), - - ### ----------------------------------- ### - ## RPARK EDIT ## - 'annotation' : annotation_str - ### ----------------------------------- ### - - } - # Add post-job actions to step dict. - if module.type == 'tool': - pja_dict = {} - for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, - output_name = pja.output_name, - action_arguments = pja.action_arguments ) - step_dict[ 'post_job_actions' ] = pja_dict - # Data inputs - step_dict['inputs'] = [] - if module.type == "data_input": - # Get input dataset name; default to 'Input Dataset' - name = module.state.get( 'name', 'Input Dataset') - step_dict['inputs'].append( { "name" : name, "description" : annotation_str } ) - else: - # Step is a tool and may have runtime inputs. - for name, val in module.state.inputs.items(): - input_type = type( val ) - if input_type == RuntimeValue: - step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - elif input_type == dict: - # Input type is described by a dict, e.g. indexed parameters. - for partval in val.values(): - if type( partval ) == RuntimeValue: - step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - # User outputs - step_dict['user_outputs'] = [] - """ - module_outputs = module.get_data_outputs() - step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step ) - for output in step_outputs: - name = output.output_name - annotation = "" - for module_output in module_outputs: - if module_output.get( 'name', None ) == name: - output_type = module_output.get( 'extension', '' ) - break - data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type } - """ - - # All step outputs - step_dict['outputs'] = [] - if type( module ) is ToolModule: - for output in module.get_data_outputs(): - step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) - # Connections - input_connections = step.input_connections - if step.type is None or step.type == 'tool': - # Determine full (prefixed) names of valid input datasets - data_input_names = {} - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - data_input_names[ prefixed_name ] = True - visit_input_values( module.tool.inputs, module.state.inputs, callback ) - # Filter - # FIXME: this removes connection without displaying a message currently! - input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] - # Encode input connections as dictionary - input_conn_dict = {} - for conn in input_connections: - input_conn_dict[ conn.input_name ] = \ - dict( id=conn.output_step.order_index, output_name=conn.output_name ) - step_dict['input_connections'] = input_conn_dict - # Position - step_dict['position'] = step.position - # Add to return value - data['steps'][step.order_index] = step_dict - return data - @expose_api def import_shared_workflow(self, trans, payload, **kwd): """ diff -r 1f91923153d2d64a216ddbeb06810df3ac12be06 -r 7ed68c60b4546c90f24f4463b644f6fffe712596 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -21,7 +21,7 @@ from galaxy.jobs.actions.post import ActionBox from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc -from galaxy.tools.parameters import RuntimeValue, visit_input_values +from galaxy.tools.parameters import visit_input_values from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue from galaxy.tools.parameters.grouping import Conditional, Repeat from galaxy.util.odict import odict @@ -32,7 +32,7 @@ from galaxy.web.framework import form from galaxy.web.framework.helpers import grids, time_ago from galaxy.web.framework.helpers import to_unicode -from galaxy.workflow.modules import module_factory, ToolModule +from galaxy.workflow.modules import module_factory class StoredWorkflowListGrid( grids.Grid ): @@ -1608,131 +1608,6 @@ shared_by_others=shared_by_others, ids_in_menu=ids_in_menu ) - def _workflow_to_dict( self, trans, stored ): - """ - Converts a workflow to a dict of attributes suitable for exporting. - """ - workflow = stored.latest_workflow - workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored ) - annotation_str = "" - if workflow_annotation: - annotation_str = workflow_annotation.annotation - # Pack workflow data into a dictionary and return - data = {} - data['a_galaxy_workflow'] = 'true' # Placeholder for identifying galaxy workflow - data['format-version'] = "0.1" - data['name'] = workflow.name - data['annotation'] = annotation_str - data['steps'] = {} - # For each step, rebuild the form and encode the state - for step in workflow.steps: - # Load from database representation - module = module_factory.from_workflow_step( trans, step ) - if not module: - return None - # Get user annotation. - step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) - annotation_str = "" - if step_annotation: - annotation_str = step_annotation.annotation - # Step info - step_dict = { - 'id': step.order_index, - 'type': module.type, - 'tool_id': module.get_tool_id(), - 'tool_version' : step.tool_version, - 'name': module.get_name(), - 'tool_state': module.get_state( secure=False ), - 'tool_errors': module.get_errors(), - ## 'data_inputs': module.get_data_inputs(), - ## 'data_outputs': module.get_data_outputs(), - 'annotation' : annotation_str - } - # Add post-job actions to step dict. - if module.type == 'tool': - pja_dict = {} - for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, - output_name = pja.output_name, - action_arguments = pja.action_arguments ) - step_dict[ 'post_job_actions' ] = pja_dict - # Data inputs - step_dict['inputs'] = [] - if module.type == "data_input": - # Get input dataset name; default to 'Input Dataset' - name = module.state.get( 'name', 'Input Dataset') - step_dict['inputs'].append( { "name" : name, "description" : annotation_str } ) - else: - # Step is a tool and may have runtime inputs. - for name, val in module.state.inputs.items(): - input_type = type( val ) - if input_type == RuntimeValue: - step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - elif input_type == dict: - # Input type is described by a dict, e.g. indexed parameters. - for partname, partval in val.items(): - if type( partval ) == RuntimeValue: - step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - # User outputs - step_dict['user_outputs'] = [] - """ - module_outputs = module.get_data_outputs() - step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step ) - for output in step_outputs: - name = output.output_name - annotation = "" - for module_output in module_outputs: - if module_output.get( 'name', None ) == name: - output_type = module_output.get( 'extension', '' ) - break - data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type } - """ - - # All step outputs - step_dict['outputs'] = [] - if type( module ) is ToolModule: - for output in module.get_data_outputs(): - step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) - # Connections - input_connections = step.input_connections - if step.type is None or step.type == 'tool': - # Determine full (prefixed) names of valid input datasets - data_input_names = {} - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - data_input_names[ prefixed_name ] = True - - # FIXME: this updates modules silently right now; messages from updates should be provided. - module.check_and_update_state() - visit_input_values( module.tool.inputs, module.state.inputs, callback ) - # Filter - # FIXME: this removes connection without displaying a message currently! - input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] - # Encode input connections as dictionary - input_conn_dict = {} - unique_input_names = set( [conn.input_name for conn in input_connections] ) - for input_name in unique_input_names: - input_conn_dict[ input_name ] = \ - [ dict( id=conn.output_step.order_index, output_name=conn.output_name ) for conn in input_connections if conn.input_name == input_name ] - # Preserve backward compatability. Previously Galaxy - # assumed input connections would be dictionaries not - # lists of dictionaries, so replace any singleton list - # with just the dictionary so that workflows exported from - # newer Galaxy instances can be used with older Galaxy - # instances if they do no include multiple input - # tools. This should be removed at some point. Mirrored - # hack in _workflow_from_dict should never be removed so - # existing workflow exports continue to function. - for input_name, input_conn in dict(input_conn_dict).iteritems(): - if len(input_conn) == 1: - input_conn_dict[input_name] = input_conn[0] - step_dict['input_connections'] = input_conn_dict - # Position - step_dict['position'] = step.position - # Add to return value - data['steps'][step.order_index] = step_dict - return data - def _workflow_to_svg_canvas( self, trans, stored ): workflow = stored.latest_workflow data = [] https://bitbucket.org/galaxy/galaxy-central/commits/8c98ef649bc0/ Changeset: 8c98ef649bc0 User: nsoranzo Date: 2014-01-24 16:05:27 Summary: Fix typo in action name. Affected #: 1 file diff -r 7ed68c60b4546c90f24f4463b644f6fffe712596 -r 8c98ef649bc0f94edf72c9adbff3947243ad33de lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -167,7 +167,7 @@ webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) - webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_worflow', conditions=dict( method=['POST'] ) ) + webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_workflow', conditions=dict( method=['POST'] ) ) # ============================ # ===== AUTHENTICATE API ===== https://bitbucket.org/galaxy/galaxy-central/commits/51798d8a3c92/ Changeset: 51798d8a3c92 User: jmchilton Date: 2014-01-25 17:27:04 Summary: Merged in nsoranzo/galaxy-central (pull request #306) Fix typo and reduce duplication in workflow API Affected #: 4 files diff -r 122fe556dc384291119115d096210e4298e43f93 -r 51798d8a3c92a2290537f6dcfb8f93e6f1371509 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -5,16 +5,12 @@ import operator import os import re -import urllib from gettext import gettext import pkg_resources pkg_resources.require("SQLAlchemy >= 0.4") from sqlalchemy import func, and_, select -pkg_resources.require( "Routes" ) -import routes - from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError from paste.httpexceptions import HTTPNotImplemented, HTTPRequestRangeNotSatisfiable from galaxy.exceptions import ItemAccessibilityException, ItemDeletionException, ItemOwnershipException @@ -40,8 +36,11 @@ from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation, HistoryDatasetAssociation -from galaxy.datatypes.display_applications import util as da_util from galaxy.datatypes.metadata import FileParameter +from galaxy.tools.parameters import RuntimeValue, visit_input_values +from galaxy.tools.parameters.basic import DataToolParameter +from galaxy.util.json import to_json_string +from galaxy.workflow.modules import ToolModule log = logging.getLogger( __name__ ) @@ -1559,6 +1558,227 @@ session.flush() return imported_stored + def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): + """ + Creates a workflow from a dict. Created workflow is stored in the database and returned. + """ + from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps + + # Put parameters in workflow mode + trans.workflow_building_mode = True + # Create new workflow from incoming dict + workflow = model.Workflow() + # If there's a source, put it in the workflow name. + if source: + name = "%s (imported from %s)" % ( data['name'], source ) + else: + name = data['name'] + workflow.name = name + # Assume no errors until we find a step that has some + workflow.has_errors = False + # Create each step + steps = [] + # The editor will provide ids for each step that we don't need to save, + # but do need to use to make connections + steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the local Galaxy instance. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] + # First pass to build step objects and populate basic values + for step_dict in data[ 'steps' ].itervalues(): + # Create the model class for the step + step = model.WorkflowStep() + steps.append( step ) + steps_by_external_id[ step_dict['id' ] ] = step + # FIXME: Position should be handled inside module + step.position = step_dict['position'] + module = module_factory.from_dict( trans, step_dict, secure=False ) + module.save_to_step( step ) + if module.type == 'tool' and module.tool is None: + # A required tool is not available in the local Galaxy instance. + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) + # Save the entire step_dict in the unused config field, be parsed later + # when we do have the tool + step.config = to_json_string(step_dict) + if step.tool_errors: + workflow.has_errors = True + # Stick this in the step temporarily + step.temp_input_connections = step_dict['input_connections'] + # Save step annotation. + annotation = step_dict[ 'annotation' ] + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) + # Second pass to deal with connections between steps + for step in steps: + # Input connections + for input_name, conn_list in step.temp_input_connections.iteritems(): + if not conn_list: + continue + if not isinstance(conn_list, list): # Older style singleton connection + conn_list = [conn_list] + for conn_dict in conn_list: + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_name = conn_dict['output_name'] + conn.output_step = steps_by_external_id[ conn_dict['id'] ] + del step.temp_input_connections + + # Order the steps if possible + attach_ordered_steps( workflow, steps ) + + # Connect up + stored = model.StoredWorkflow() + stored.name = workflow.name + workflow.stored_workflow = stored + stored.latest_workflow = workflow + stored.user = trans.user + if data[ 'annotation' ]: + self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) + + # Persist + trans.sa_session.add( stored ) + trans.sa_session.flush() + + if add_to_menu: + if trans.user.stored_workflow_menu_entries == None: + trans.user.stored_workflow_menu_entries = [] + menuEntry = model.StoredWorkflowMenuEntry() + menuEntry.stored_workflow = stored + trans.user.stored_workflow_menu_entries.append( menuEntry ) + trans.sa_session.flush() + + return stored, missing_tool_tups + + def _workflow_to_dict( self, trans, stored ): + """ + Converts a workflow to a dict of attributes suitable for exporting. + """ + workflow = stored.latest_workflow + workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored ) + annotation_str = "" + if workflow_annotation: + annotation_str = workflow_annotation.annotation + # Pack workflow data into a dictionary and return + data = {} + data['a_galaxy_workflow'] = 'true' # Placeholder for identifying galaxy workflow + data['format-version'] = "0.1" + data['name'] = workflow.name + data['annotation'] = annotation_str + data['steps'] = {} + # For each step, rebuild the form and encode the state + for step in workflow.steps: + # Load from database representation + module = module_factory.from_workflow_step( trans, step ) + if not module: + return None + # Get user annotation. + step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) + annotation_str = "" + if step_annotation: + annotation_str = step_annotation.annotation + # Step info + step_dict = { + 'id': step.order_index, + 'type': module.type, + 'tool_id': module.get_tool_id(), + 'tool_version' : step.tool_version, + 'name': module.get_name(), + 'tool_state': module.get_state( secure=False ), + 'tool_errors': module.get_errors(), + ## 'data_inputs': module.get_data_inputs(), + ## 'data_outputs': module.get_data_outputs(), + 'annotation' : annotation_str + } + # Add post-job actions to step dict. + if module.type == 'tool': + pja_dict = {} + for pja in step.post_job_actions: + pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, + output_name = pja.output_name, + action_arguments = pja.action_arguments ) + step_dict[ 'post_job_actions' ] = pja_dict + # Data inputs + step_dict['inputs'] = [] + if module.type == "data_input": + # Get input dataset name; default to 'Input Dataset' + name = module.state.get( 'name', 'Input Dataset') + step_dict['inputs'].append( { "name" : name, "description" : annotation_str } ) + else: + # Step is a tool and may have runtime inputs. + for name, val in module.state.inputs.items(): + input_type = type( val ) + if input_type == RuntimeValue: + step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) + elif input_type == dict: + # Input type is described by a dict, e.g. indexed parameters. + for partval in val.values(): + if type( partval ) == RuntimeValue: + step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) + # User outputs + step_dict['user_outputs'] = [] + """ + module_outputs = module.get_data_outputs() + step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step ) + for output in step_outputs: + name = output.output_name + annotation = "" + for module_output in module_outputs: + if module_output.get( 'name', None ) == name: + output_type = module_output.get( 'extension', '' ) + break + data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type } + """ + + # All step outputs + step_dict['outputs'] = [] + if type( module ) is ToolModule: + for output in module.get_data_outputs(): + step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) + # Connections + input_connections = step.input_connections + if step.type is None or step.type == 'tool': + # Determine full (prefixed) names of valid input datasets + data_input_names = {} + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + data_input_names[ prefixed_name ] = True + + # FIXME: this updates modules silently right now; messages from updates should be provided. + module.check_and_update_state() + visit_input_values( module.tool.inputs, module.state.inputs, callback ) + # Filter + # FIXME: this removes connection without displaying a message currently! + input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] + # Encode input connections as dictionary + input_conn_dict = {} + unique_input_names = set( [conn.input_name for conn in input_connections] ) + for input_name in unique_input_names: + input_conn_dict[ input_name ] = \ + [ dict( id=conn.output_step.order_index, output_name=conn.output_name ) for conn in input_connections if conn.input_name == input_name ] + # Preserve backward compatability. Previously Galaxy + # assumed input connections would be dictionaries not + # lists of dictionaries, so replace any singleton list + # with just the dictionary so that workflows exported from + # newer Galaxy instances can be used with older Galaxy + # instances if they do no include multiple input + # tools. This should be removed at some point. Mirrored + # hack in _workflow_from_dict should never be removed so + # existing workflow exports continue to function. + for input_name, input_conn in dict(input_conn_dict).iteritems(): + if len(input_conn) == 1: + input_conn_dict[input_name] = input_conn[0] + step_dict['input_connections'] = input_conn_dict + # Position + step_dict['position'] = step.position + # Add to return value + data['steps'][step.order_index] = step_dict + return data + class UsesFormDefinitionsMixin: """Mixin for controllers that use Galaxy form objects.""" diff -r 122fe556dc384291119115d096210e4298e43f93 -r 51798d8a3c92a2290537f6dcfb8f93e6f1371509 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -9,14 +9,12 @@ from galaxy import exceptions from galaxy import util from galaxy import web -from galaxy import model -from galaxy.tools.parameters import visit_input_values, DataToolParameter, RuntimeValue +from galaxy.tools.parameters import visit_input_values, DataToolParameter from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin -from galaxy.workflow.modules import module_factory, ToolModule +from galaxy.workflow.modules import module_factory from galaxy.jobs.actions.post import ActionBox -from ..controllers.workflow import attach_ordered_steps log = logging.getLogger(__name__) @@ -367,226 +365,8 @@ return item - def _workflow_from_dict( self, trans, data, source=None ): - """ - RPARK: copied from galaxy.webapps.galaxy.controllers.workflows.py - Creates a workflow from a dict. Created workflow is stored in the database and returned. - """ - # Put parameters in workflow mode - trans.workflow_building_mode = True - # Create new workflow from incoming dict - workflow = model.Workflow() - # If there's a source, put it in the workflow name. - if source: - name = "%s (imported from %s)" % ( data['name'], source ) - else: - name = data['name'] - workflow.name = name - # Assume no errors until we find a step that has some - workflow.has_errors = False - # Create each step - steps = [] - # The editor will provide ids for each step that we don't need to save, - # but do need to use to make connections - steps_by_external_id = {} - # Keep track of tools required by the workflow that are not available in - # the local Galaxy instance. Each tuple in the list of missing_tool_tups - # will be ( tool_id, tool_name, tool_version ). - missing_tool_tups = [] - # First pass to build step objects and populate basic values - for step_dict in data[ 'steps' ].itervalues(): - # Create the model class for the step - step = model.WorkflowStep() - steps.append( step ) - steps_by_external_id[ step_dict['id' ] ] = step - # FIXME: Position should be handled inside module - step.position = step_dict['position'] - module = module_factory.from_dict( trans, step_dict, secure=False ) - if module.type == 'tool' and module.tool is None: - # A required tool is not available in the local Galaxy instance. - missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) - if missing_tool_tup not in missing_tool_tups: - missing_tool_tups.append( missing_tool_tup ) - module.save_to_step( step ) - if step.tool_errors: - workflow.has_errors = True - # Stick this in the step temporarily - step.temp_input_connections = step_dict['input_connections'] - # Save step annotation. - #annotation = step_dict[ 'annotation' ] - #if annotation: - #annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - # ------------------------------------------ # - # RPARK REMOVING: user annotation b/c of API - #self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) - # ------------------------------------------ # - # Unpack and add post-job actions. - post_job_actions = step_dict.get( 'post_job_actions', {} ) - for name, pja_dict in post_job_actions.items(): - model.PostJobAction( pja_dict[ 'action_type' ], - step, pja_dict[ 'output_name' ], - pja_dict[ 'action_arguments' ] ) - # Second pass to deal with connections between steps - for step in steps: - # Input connections - for input_name, conn_dict in step.temp_input_connections.iteritems(): - if conn_dict: - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] - del step.temp_input_connections - # Order the steps if possible - attach_ordered_steps( workflow, steps ) - # Connect up - stored = model.StoredWorkflow() - stored.name = workflow.name - workflow.stored_workflow = stored - stored.latest_workflow = workflow - stored.user = trans.user - # Persist - trans.sa_session.add( stored ) - trans.sa_session.flush() - return stored, missing_tool_tups - - def _workflow_to_dict( self, trans, stored ): - """ - RPARK: copied from galaxy.web.controllers.workflows.py - Converts a workflow to a dict of attributes suitable for exporting. - """ - workflow = stored.latest_workflow - - ### ----------------------------------- ### - ## RPARK EDIT ## - workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored ) - annotation_str = "" - if workflow_annotation: - annotation_str = workflow_annotation.annotation - ### ----------------------------------- ### - - - # Pack workflow data into a dictionary and return - data = {} - data['a_galaxy_workflow'] = 'true' # Placeholder for identifying galaxy workflow - data['format-version'] = "0.1" - data['name'] = workflow.name - ### ----------------------------------- ### - ## RPARK EDIT ## - data['annotation'] = annotation_str - ### ----------------------------------- ### - - data['steps'] = {} - # For each step, rebuild the form and encode the state - for step in workflow.steps: - # Load from database representation - module = module_factory.from_workflow_step( trans, step ) - if not module: - return None - - ### ----------------------------------- ### - ## RPARK EDIT ## - - # TODO: This is duplicated from - # lib/galaxy/webapps/controllres/workflow.py -- refactor and - # eliminate copied code. - - # Get user annotation. - step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) - annotation_str = "" - if step_annotation: - annotation_str = step_annotation.annotation - ### ----------------------------------- ### - - # Step info - step_dict = { - 'id': step.order_index, - 'type': module.type, - 'tool_id': module.get_tool_id(), - 'tool_version' : step.tool_version, - 'name': module.get_name(), - 'tool_state': module.get_state( secure=False ), - 'tool_errors': module.get_errors(), - ## 'data_inputs': module.get_data_inputs(), - ## 'data_outputs': module.get_data_outputs(), - - ### ----------------------------------- ### - ## RPARK EDIT ## - 'annotation' : annotation_str - ### ----------------------------------- ### - - } - # Add post-job actions to step dict. - if module.type == 'tool': - pja_dict = {} - for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, - output_name = pja.output_name, - action_arguments = pja.action_arguments ) - step_dict[ 'post_job_actions' ] = pja_dict - # Data inputs - step_dict['inputs'] = [] - if module.type == "data_input": - # Get input dataset name; default to 'Input Dataset' - name = module.state.get( 'name', 'Input Dataset') - step_dict['inputs'].append( { "name" : name, "description" : annotation_str } ) - else: - # Step is a tool and may have runtime inputs. - for name, val in module.state.inputs.items(): - input_type = type( val ) - if input_type == RuntimeValue: - step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - elif input_type == dict: - # Input type is described by a dict, e.g. indexed parameters. - for partval in val.values(): - if type( partval ) == RuntimeValue: - step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - # User outputs - step_dict['user_outputs'] = [] - """ - module_outputs = module.get_data_outputs() - step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step ) - for output in step_outputs: - name = output.output_name - annotation = "" - for module_output in module_outputs: - if module_output.get( 'name', None ) == name: - output_type = module_output.get( 'extension', '' ) - break - data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type } - """ - - # All step outputs - step_dict['outputs'] = [] - if type( module ) is ToolModule: - for output in module.get_data_outputs(): - step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) - # Connections - input_connections = step.input_connections - if step.type is None or step.type == 'tool': - # Determine full (prefixed) names of valid input datasets - data_input_names = {} - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - data_input_names[ prefixed_name ] = True - visit_input_values( module.tool.inputs, module.state.inputs, callback ) - # Filter - # FIXME: this removes connection without displaying a message currently! - input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] - # Encode input connections as dictionary - input_conn_dict = {} - for conn in input_connections: - input_conn_dict[ conn.input_name ] = \ - dict( id=conn.output_step.order_index, output_name=conn.output_name ) - step_dict['input_connections'] = input_conn_dict - # Position - step_dict['position'] = step.position - # Add to return value - data['steps'][step.order_index] = step_dict - return data - @expose_api - def import_shared_worflow(self, trans, payload, **kwd): + def import_shared_workflow(self, trans, payload, **kwd): """ POST /api/workflows/import Import a workflow shared by other users. diff -r 122fe556dc384291119115d096210e4298e43f93 -r 51798d8a3c92a2290537f6dcfb8f93e6f1371509 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -167,7 +167,7 @@ webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) - webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_worflow', conditions=dict( method=['POST'] ) ) + webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_workflow', conditions=dict( method=['POST'] ) ) # ============================ # ===== AUTHENTICATE API ===== diff -r 122fe556dc384291119115d096210e4298e43f93 -r 51798d8a3c92a2290537f6dcfb8f93e6f1371509 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -21,10 +21,9 @@ from galaxy.jobs.actions.post import ActionBox from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc -from galaxy.tools.parameters import RuntimeValue, visit_input_values +from galaxy.tools.parameters import visit_input_values from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue from galaxy.tools.parameters.grouping import Conditional, Repeat -from galaxy.util.json import to_json_string from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html from galaxy.util.topsort import CycleError, topsort, topsort_levels @@ -33,7 +32,7 @@ from galaxy.web.framework import form from galaxy.web.framework.helpers import grids, time_ago from galaxy.web.framework.helpers import to_unicode -from galaxy.workflow.modules import module_factory, ToolModule +from galaxy.workflow.modules import module_factory class StoredWorkflowListGrid( grids.Grid ): @@ -1609,225 +1608,6 @@ shared_by_others=shared_by_others, ids_in_menu=ids_in_menu ) - def _workflow_to_dict( self, trans, stored ): - """ - Converts a workflow to a dict of attributes suitable for exporting. - """ - workflow = stored.latest_workflow - workflow_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, stored ) - annotation_str = "" - if workflow_annotation: - annotation_str = workflow_annotation.annotation - # Pack workflow data into a dictionary and return - data = {} - data['a_galaxy_workflow'] = 'true' # Placeholder for identifying galaxy workflow - data['format-version'] = "0.1" - data['name'] = workflow.name - data['annotation'] = annotation_str - data['steps'] = {} - # For each step, rebuild the form and encode the state - for step in workflow.steps: - # Load from database representation - module = module_factory.from_workflow_step( trans, step ) - if not module: - return None - # Get user annotation. - step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) - annotation_str = "" - if step_annotation: - annotation_str = step_annotation.annotation - # Step info - step_dict = { - 'id': step.order_index, - 'type': module.type, - 'tool_id': module.get_tool_id(), - 'tool_version' : step.tool_version, - 'name': module.get_name(), - 'tool_state': module.get_state( secure=False ), - 'tool_errors': module.get_errors(), - ## 'data_inputs': module.get_data_inputs(), - ## 'data_outputs': module.get_data_outputs(), - 'annotation' : annotation_str - } - # Add post-job actions to step dict. - if module.type == 'tool': - pja_dict = {} - for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, - output_name = pja.output_name, - action_arguments = pja.action_arguments ) - step_dict[ 'post_job_actions' ] = pja_dict - # Data inputs - step_dict['inputs'] = [] - if module.type == "data_input": - # Get input dataset name; default to 'Input Dataset' - name = module.state.get( 'name', 'Input Dataset') - step_dict['inputs'].append( { "name" : name, "description" : annotation_str } ) - else: - # Step is a tool and may have runtime inputs. - for name, val in module.state.inputs.items(): - input_type = type( val ) - if input_type == RuntimeValue: - step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - elif input_type == dict: - # Input type is described by a dict, e.g. indexed parameters. - for partname, partval in val.items(): - if type( partval ) == RuntimeValue: - step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - # User outputs - step_dict['user_outputs'] = [] - """ - module_outputs = module.get_data_outputs() - step_outputs = trans.sa_session.query( WorkflowOutput ).filter( step=step ) - for output in step_outputs: - name = output.output_name - annotation = "" - for module_output in module_outputs: - if module_output.get( 'name', None ) == name: - output_type = module_output.get( 'extension', '' ) - break - data['outputs'][name] = { 'name' : name, 'annotation' : annotation, 'type' : output_type } - """ - - # All step outputs - step_dict['outputs'] = [] - if type( module ) is ToolModule: - for output in module.get_data_outputs(): - step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) - # Connections - input_connections = step.input_connections - if step.type is None or step.type == 'tool': - # Determine full (prefixed) names of valid input datasets - data_input_names = {} - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - data_input_names[ prefixed_name ] = True - - # FIXME: this updates modules silently right now; messages from updates should be provided. - module.check_and_update_state() - visit_input_values( module.tool.inputs, module.state.inputs, callback ) - # Filter - # FIXME: this removes connection without displaying a message currently! - input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] - # Encode input connections as dictionary - input_conn_dict = {} - unique_input_names = set( [conn.input_name for conn in input_connections] ) - for input_name in unique_input_names: - input_conn_dict[ input_name ] = \ - [ dict( id=conn.output_step.order_index, output_name=conn.output_name ) for conn in input_connections if conn.input_name == input_name ] - # Preserve backward compatability. Previously Galaxy - # assumed input connections would be dictionaries not - # lists of dictionaries, so replace any singleton list - # with just the dictionary so that workflows exported from - # newer Galaxy instances can be used with older Galaxy - # instances if they do no include multiple input - # tools. This should be removed at some point. Mirrored - # hack in _workflow_from_dict should never be removed so - # existing workflow exports continue to function. - for input_name, input_conn in dict(input_conn_dict).iteritems(): - if len(input_conn) == 1: - input_conn_dict[input_name] = input_conn[0] - step_dict['input_connections'] = input_conn_dict - # Position - step_dict['position'] = step.position - # Add to return value - data['steps'][step.order_index] = step_dict - return data - - def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): - """ - Creates a workflow from a dict. Created workflow is stored in the database and returned. - """ - # Put parameters in workflow mode - trans.workflow_building_mode = True - # Create new workflow from incoming dict - workflow = model.Workflow() - # If there's a source, put it in the workflow name. - if source: - name = "%s (imported from %s)" % ( data['name'], source ) - else: - name = data['name'] - workflow.name = name - # Assume no errors until we find a step that has some - workflow.has_errors = False - # Create each step - steps = [] - # The editor will provide ids for each step that we don't need to save, - # but do need to use to make connections - steps_by_external_id = {} - # Keep track of tools required by the workflow that are not available in - # the local Galaxy instance. Each tuple in the list of missing_tool_tups - # will be ( tool_id, tool_name, tool_version ). - missing_tool_tups = [] - # First pass to build step objects and populate basic values - for key, step_dict in data[ 'steps' ].iteritems(): - # Create the model class for the step - step = model.WorkflowStep() - steps.append( step ) - steps_by_external_id[ step_dict['id' ] ] = step - # FIXME: Position should be handled inside module - step.position = step_dict['position'] - module = module_factory.from_dict( trans, step_dict, secure=False ) - module.save_to_step( step ) - if module.type == 'tool' and module.tool is None: - # A required tool is not available in the local Galaxy instance. - missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) - if missing_tool_tup not in missing_tool_tups: - missing_tool_tups.append( missing_tool_tup ) - # Save the entire step_dict in the unused config field, be parsed later - # when we do have the too when we do have the tool - step.config = to_json_string(step_dict) - if step.tool_errors: - workflow.has_errors = True - # Stick this in the step temporarily - step.temp_input_connections = step_dict['input_connections'] - # Save step annotation. - annotation = step_dict[ 'annotation' ] - if annotation: - annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) - # Second pass to deal with connections between steps - for step in steps: - # Input connections - for input_name, conn_list in step.temp_input_connections.iteritems(): - if not conn_list: - continue - if not isinstance(conn_list, list): # Older style singleton connection - conn_list = [conn_list] - for conn_dict in conn_list: - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] - del step.temp_input_connections - - # Order the steps if possible - attach_ordered_steps( workflow, steps ) - - # Connect up - stored = model.StoredWorkflow() - stored.name = workflow.name - workflow.stored_workflow = stored - stored.latest_workflow = workflow - stored.user = trans.user - if data[ 'annotation' ]: - self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) - - # Persist - trans.sa_session.add( stored ) - trans.sa_session.flush() - - if add_to_menu: - if trans.user.stored_workflow_menu_entries == None: - trans.user.stored_workflow_menu_entries = [] - menuEntry = model.StoredWorkflowMenuEntry() - menuEntry.stored_workflow = stored - trans.user.stored_workflow_menu_entries.append( menuEntry ) - trans.sa_session.flush() - - return stored, missing_tool_tups - def _workflow_to_svg_canvas( self, trans, stored ): workflow = stored.latest_workflow data = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Upload: Allow backend to set file names
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/122fe556dc38/ Changeset: 122fe556dc38 User: guerler Date: 2014-01-25 06:23:19 Summary: Upload: Allow backend to set file names Affected #: 2 files diff -r c5caf4ce55aa0102b85032805ddd50445cb03002 -r 122fe556dc384291119115d096210e4298e43f93 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -372,7 +372,6 @@ tool_input = {}; tool_input['dbkey'] = genome; tool_input['file_type'] = file_type; - tool_input['files_0|NAME'] = file_name; tool_input['files_0|type'] = 'upload_dataset'; tool_input['files_0|url_paste'] = url_paste; tool_input['space_to_tabs'] = space_to_tabs; diff -r c5caf4ce55aa0102b85032805ddd50445cb03002 -r 122fe556dc384291119115d096210e4298e43f93 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;$(window).on("beforeunload",function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}})},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");g.css({width:h+"%"})},_template:function(g){return'<div class="progress-button"><div class="progress"><div class="progress-bar"></div></div><div id="label" class="label"><div class="fa '+g.icon+'"></div> '+g.label+"</div></div>"}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]<k[0]?-1:0});g.select_genome.unshift(j)});if(h){this.options=_.defaults(h,this.options)}this.collection.on("remove",function(i){g._eventRemove(i)});this.collection.on("change:genome",function(j){var i=j.get("genome");g.collection.each(function(k){if(k.get("status")=="init"&&k.get("genome")=="?"){k.set("genome",i)}})})},_eventShow:function(h){h.preventDefault();h.stopPropagation();if(!this.modal){var g=this;this.modal=new c.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose files":function(){g.uploadbox.select()},"Create file":function(){g._eventCreate()},Start:function(){g._eventStart()},Pause:function(){g._eventStop()},Reset:function(){g._eventReset()},Close:function(){g.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var g=this;this.uploadbox=this.$el.uploadbox({announce:function(i,j,k){g._eventAnnounce(i,j,k)},initialize:function(i,j,k){return g._eventInitialize(i,j,k)},progress:function(i,j,k){g._eventProgress(i,j,k)},success:function(i,j,k){g._eventSuccess(i,j,k)},error:function(i,j,k){g._eventError(i,j,k)},complete:function(){g._eventComplete()}});this._updateScreen()}this.modal.show()},_eventRemove:function(h){var g=h.get("status");if(g=="success"){this.counter.success--}else{if(g=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(h.id)},_eventAnnounce:function(g,h,j){this.counter.announce++;this._updateScreen();var i=new d(this,{id:g,file_name:h.name,file_size:h.size});this.collection.add(i.model);$(this.el).find("tbody:last").append(i.$el);i.render()},_eventInitialize:function(k,g,o){var i=this.collection.get(k);i.set("status","running");var h=i.get("extension");var l=i.get("file_name");var n=i.get("genome");var m=i.get("url_paste");var j=i.get("space_to_tabs");if(!m&&!(g.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose files");this.modal.enableButton("Create file")}else{this.modal.disableButton("Choose files");this.modal.disableButton("Create file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'<div id="'+h+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+g+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;$(window).on("beforeunload",function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}})},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");g.css({width:h+"%"})},_template:function(g){return'<div class="progress-button"><div class="progress"><div class="progress-bar"></div></div><div id="label" class="label"><div class="fa '+g.icon+'"></div> '+g.label+"</div></div>"}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]<k[0]?-1:0});g.select_genome.unshift(j)});if(h){this.options=_.defaults(h,this.options)}this.collection.on("remove",function(i){g._eventRemove(i)});this.collection.on("change:genome",function(j){var i=j.get("genome");g.collection.each(function(k){if(k.get("status")=="init"&&k.get("genome")=="?"){k.set("genome",i)}})})},_eventShow:function(h){h.preventDefault();h.stopPropagation();if(!this.modal){var g=this;this.modal=new c.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose files":function(){g.uploadbox.select()},"Create file":function(){g._eventCreate()},Start:function(){g._eventStart()},Pause:function(){g._eventStop()},Reset:function(){g._eventReset()},Close:function(){g.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var g=this;this.uploadbox=this.$el.uploadbox({announce:function(i,j,k){g._eventAnnounce(i,j,k)},initialize:function(i,j,k){return g._eventInitialize(i,j,k)},progress:function(i,j,k){g._eventProgress(i,j,k)},success:function(i,j,k){g._eventSuccess(i,j,k)},error:function(i,j,k){g._eventError(i,j,k)},complete:function(){g._eventComplete()}});this._updateScreen()}this.modal.show()},_eventRemove:function(h){var g=h.get("status");if(g=="success"){this.counter.success--}else{if(g=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(h.id)},_eventAnnounce:function(g,h,j){this.counter.announce++;this._updateScreen();var i=new d(this,{id:g,file_name:h.name,file_size:h.size});this.collection.add(i.model);$(this.el).find("tbody:last").append(i.$el);i.render()},_eventInitialize:function(k,g,o){var i=this.collection.get(k);i.set("status","running");var h=i.get("extension");var l=i.get("file_name");var n=i.get("genome");var m=i.get("url_paste");var j=i.get("space_to_tabs");if(!m&&!(g.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose files");this.modal.enableButton("Create file")}else{this.modal.disableButton("Choose files");this.modal.disableButton("Create file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'<div id="'+h+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+g+'" class="upload-info"></h6>'}})}); \ 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: Webhelpers: Shorten time ago string
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c5caf4ce55aa/ Changeset: c5caf4ce55aa User: guerler Date: 2014-01-25 06:07:12 Summary: Webhelpers: Shorten time ago string Affected #: 1 file diff -r 4362d887f48fe1891f46fc1ee435045b79c3779a -r c5caf4ce55aa0102b85032805ddd50445cb03002 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -28,7 +28,8 @@ if (datetime.utcnow() - x) > delta: # Greater than a week difference return x.strftime("%b %d, %Y") else: - return date.distance_of_time_in_words( x, datetime.utcnow() ).replace("about", "~") + " ago" + date_array = date.distance_of_time_in_words( x, datetime.utcnow() ).replace(",", "").split(" ") + return "~%s %s ago" % (date_array[0], date_array[1]) def iff( a, b, c ): """ 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: Reduce line height
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4362d887f48f/ Changeset: 4362d887f48f User: guerler Date: 2014-01-25 00:12:47 Summary: Upload: Reduce line height Affected #: 2 files diff -r b48698ef4da4976dcd177e81a6e45381310337c6 -r 4362d887f48fe1891f46fc1ee435045b79c3779a static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1255,7 +1255,7 @@ .progress-button .progress-bar-success{background:#aff1af;border:0px} .progress-button .progress-bar-info{background:#ffc} .progress-button .progress-bar-notransition{-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none} -.progress-button .label{position:absolute;top:0px;width:inherit;text-align:center;line-height:20px} +.progress-button .label{position:absolute;top:0px;width:inherit;text-align:center;line-height:19px} .upload-info{font-weight:normal;text-align:center} .upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%} .upload-box .table th{text-align:center;white-space:nowrap} diff -r b48698ef4da4976dcd177e81a6e45381310337c6 -r 4362d887f48fe1891f46fc1ee435045b79c3779a static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -39,7 +39,7 @@ top: 0px; width: inherit; text-align: center; - line-height: 20px; + line-height: 19px; } } 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: Improve progress button styles
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b48698ef4da4/ Changeset: b48698ef4da4 User: guerler Date: 2014-01-25 00:08:37 Summary: Upload: Improve progress button styles Affected #: 4 files diff -r b7c11187252fd308a1c0878f33cc8742c9287eaa -r b48698ef4da4976dcd177e81a6e45381310337c6 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -93,7 +93,8 @@ '<div class="progress">' + '<div class="progress-bar"></div>' + '</div>' + - '<div id="label" class="label" style="position: absolute; top: 0px; width: inherit; text-align: center;"><div class="fa ' + options.icon + '"></div> ' + options.label + '</div>' + + '<div id="label" class="label">' + + '<div class="fa ' + options.icon + '"></div> ' + options.label + '</div>' + '</div>'; } }); diff -r b7c11187252fd308a1c0878f33cc8742c9287eaa -r b48698ef4da4976dcd177e81a6e45381310337c6 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;$(window).on("beforeunload",function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}})},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");g.css({width:h+"%"})},_template:function(g){return'<div class="progress-button"><div class="progress"><div class="progress-bar"></div></div><div id="label" class="label" style="position: absolute; top: 0px; width: inherit; text-align: center;"><div class="fa '+g.icon+'"></div> '+g.label+"</div></div>"}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]<k[0]?-1:0});g.select_genome.unshift(j)});if(h){this.options=_.defaults(h,this.options)}this.collection.on("remove",function(i){g._eventRemove(i)});this.collection.on("change:genome",function(j){var i=j.get("genome");g.collection.each(function(k){if(k.get("status")=="init"&&k.get("genome")=="?"){k.set("genome",i)}})})},_eventShow:function(h){h.preventDefault();h.stopPropagation();if(!this.modal){var g=this;this.modal=new c.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose files":function(){g.uploadbox.select()},"Create file":function(){g._eventCreate()},Start:function(){g._eventStart()},Pause:function(){g._eventStop()},Reset:function(){g._eventReset()},Close:function(){g.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var g=this;this.uploadbox=this.$el.uploadbox({announce:function(i,j,k){g._eventAnnounce(i,j,k)},initialize:function(i,j,k){return g._eventInitialize(i,j,k)},progress:function(i,j,k){g._eventProgress(i,j,k)},success:function(i,j,k){g._eventSuccess(i,j,k)},error:function(i,j,k){g._eventError(i,j,k)},complete:function(){g._eventComplete()}});this._updateScreen()}this.modal.show()},_eventRemove:function(h){var g=h.get("status");if(g=="success"){this.counter.success--}else{if(g=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(h.id)},_eventAnnounce:function(g,h,j){this.counter.announce++;this._updateScreen();var i=new d(this,{id:g,file_name:h.name,file_size:h.size});this.collection.add(i.model);$(this.el).find("tbody:last").append(i.$el);i.render()},_eventInitialize:function(k,g,o){var i=this.collection.get(k);i.set("status","running");var h=i.get("extension");var l=i.get("file_name");var n=i.get("genome");var m=i.get("url_paste");var j=i.get("space_to_tabs");if(!m&&!(g.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose files");this.modal.enableButton("Create file")}else{this.modal.disableButton("Choose files");this.modal.disableButton("Create file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'<div id="'+h+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+g+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;$(window).on("beforeunload",function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}})},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");g.css({width:h+"%"})},_template:function(g){return'<div class="progress-button"><div class="progress"><div class="progress-bar"></div></div><div id="label" class="label"><div class="fa '+g.icon+'"></div> '+g.label+"</div></div>"}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]<k[0]?-1:0});g.select_genome.unshift(j)});if(h){this.options=_.defaults(h,this.options)}this.collection.on("remove",function(i){g._eventRemove(i)});this.collection.on("change:genome",function(j){var i=j.get("genome");g.collection.each(function(k){if(k.get("status")=="init"&&k.get("genome")=="?"){k.set("genome",i)}})})},_eventShow:function(h){h.preventDefault();h.stopPropagation();if(!this.modal){var g=this;this.modal=new c.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose files":function(){g.uploadbox.select()},"Create file":function(){g._eventCreate()},Start:function(){g._eventStart()},Pause:function(){g._eventStop()},Reset:function(){g._eventReset()},Close:function(){g.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var g=this;this.uploadbox=this.$el.uploadbox({announce:function(i,j,k){g._eventAnnounce(i,j,k)},initialize:function(i,j,k){return g._eventInitialize(i,j,k)},progress:function(i,j,k){g._eventProgress(i,j,k)},success:function(i,j,k){g._eventSuccess(i,j,k)},error:function(i,j,k){g._eventError(i,j,k)},complete:function(){g._eventComplete()}});this._updateScreen()}this.modal.show()},_eventRemove:function(h){var g=h.get("status");if(g=="success"){this.counter.success--}else{if(g=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(h.id)},_eventAnnounce:function(g,h,j){this.counter.announce++;this._updateScreen();var i=new d(this,{id:g,file_name:h.name,file_size:h.size});this.collection.add(i.model);$(this.el).find("tbody:last").append(i.$el);i.render()},_eventInitialize:function(k,g,o){var i=this.collection.get(k);i.set("status","running");var h=i.get("extension");var l=i.get("file_name");var n=i.get("genome");var m=i.get("url_paste");var j=i.get("space_to_tabs");if(!m&&!(g.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose files");this.modal.enableButton("Create file")}else{this.modal.disableButton("Choose files");this.modal.disableButton("Create file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'<div id="'+h+'" class="upload-box"><table class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Space→Tab</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+g+'" class="upload-info"></h6>'}})}); \ No newline at end of file diff -r b7c11187252fd308a1c0878f33cc8742c9287eaa -r b48698ef4da4976dcd177e81a6e45381310337c6 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1250,10 +1250,12 @@ .galaxy-frame .frame .f-close{right:5px;top:3px} .galaxy-frame .frame .f-pin{left:6px;top:3px} .galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px} -.progress-button{position:absolute;width:100px;right:10px;top:6px;cursor:pointer;height:19px;border:1px solid #aaa;-moz-border-radius:3px;border-radius:3px}.progress-button .progress-bar-danger{background:#f9c7c5} +.progress-button{position:absolute;width:100px;right:10px;top:5px;cursor:pointer;height:20px;border:1px solid #aaa;-moz-border-radius:3px;border-radius:3px}.progress-button .progress{height:18px} +.progress-button .progress-bar-danger{background:#f9c7c5} .progress-button .progress-bar-success{background:#aff1af;border:0px} .progress-button .progress-bar-info{background:#ffc} .progress-button .progress-bar-notransition{-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none} +.progress-button .label{position:absolute;top:0px;width:inherit;text-align:center;line-height:20px} .upload-info{font-weight:normal;text-align:center} .upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%} .upload-box .table th{text-align:center;white-space:nowrap} diff -r b7c11187252fd308a1c0878f33cc8742c9287eaa -r b48698ef4da4976dcd177e81a6e45381310337c6 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -2,13 +2,17 @@ position: absolute; width: 100px; right: 10px; - top: 6px; + top: 5px; cursor: pointer; - height: 19px; + height: 20px; border: 1px solid @input-border; -moz-border-radius: @border-radius-base; border-radius: @border-radius-base; + .progress { + height: 18px; + } + .progress-bar-danger { background: @state-danger-bg; } @@ -29,6 +33,14 @@ -o-transition: none; transition: none; } + + .label { + position: absolute; + top: 0px; + width: inherit; + text-align: center; + line-height: 20px; + } } .upload-info { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: UI: Increase minimum sidebar width
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b7c11187252f/ Changeset: b7c11187252f User: guerler Date: 2014-01-24 23:49:22 Summary: UI: Increase minimum sidebar width Affected #: 2 files diff -r 9b337a87d6eca3bf9f7448d49337d231e3b4582b -r b7c11187252fd308a1c0878f33cc8742c9287eaa static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -11,7 +11,7 @@ // Panels -var MIN_PANEL_WIDTH = 150, +var MIN_PANEL_WIDTH = 160, MAX_PANEL_WIDTH = 800; var Panel = function( options ) { diff -r 9b337a87d6eca3bf9f7448d49337d231e3b4582b -r b7c11187252fd308a1c0878f33cc8742c9287eaa static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop;this.$header.find(".close").on("click",d.proxy(this.hide,this))};d.extend(f.prototype,{setContent:function(p){this.$header.hide();if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}if(p.closeButton){this.$header.find(".close").show();this.$header.show()}else{this.$header.find(".close").hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='progress-bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-this.$footer.outerHeight()-this.$header.outerHeight()-parseInt(this.$dialog.css("padding-top"),10)-parseInt(this.$dialog.css("padding-bottom"),10))}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});m.setContent({closeButton:true,title:" ",body:d("<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>")});m.show({backdrop:true})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=160,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop;this.$header.find(".close").on("click",d.proxy(this.hide,this))};d.extend(f.prototype,{setContent:function(p){this.$header.hide();if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}if(p.closeButton){this.$header.find(".close").show();this.$header.show()}else{this.$header.find(".close").hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='progress-bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-this.$footer.outerHeight()-this.$header.outerHeight()-parseInt(this.$dialog.css("padding-top"),10)-parseInt(this.$dialog.css("padding-bottom"),10))}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function 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commit/galaxy-central: inithello: Don't sync the filesystem with the database when running a tool migration install script.
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b337a87d6ec/ Changeset: 9b337a87d6ec User: inithello Date: 2014-01-24 22:38:43 Summary: Don't sync the filesystem with the database when running a tool migration install script. Affected #: 6 files diff -r cce4687a7ccc56a47db95498b0ae86f0f5986125 -r 9b337a87d6eca3bf9f7448d49337d231e3b4582b lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -445,7 +445,8 @@ installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies ) + tool_dependencies=tool_dependencies, + from_install_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR: text = util.unicodify( installed_tool_dependency.error_message ) diff -r cce4687a7ccc56a47db95498b0ae86f0f5986125 -r 9b337a87d6eca3bf9f7448d49337d231e3b4582b lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -440,7 +440,8 @@ installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=self.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies ) + tool_dependencies=tool_dependencies, + from_install_manager=True ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe following error occurred from the InstallManager while installing tool dependency ', installed_tool_dependency.name, ':' diff -r cce4687a7ccc56a47db95498b0ae86f0f5986125 -r 9b337a87d6eca3bf9f7448d49337d231e3b4582b lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -596,7 +596,8 @@ installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_shed_repository.tool_dependencies ) + tool_dependencies=tool_shed_repository.tool_dependencies, + from_install_manager=False ) suc.remove_dir( work_dir ) suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, @@ -841,7 +842,8 @@ installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app, tool_shed_repository=repository, tool_dependencies_config=tool_dependencies_config, - tool_dependencies=repository.tool_dependencies ) + tool_dependencies=repository.tool_dependencies, + from_install_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.ERROR ]: repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message ) diff -r cce4687a7ccc56a47db95498b0ae86f0f5986125 -r 9b337a87d6eca3bf9f7448d49337d231e3b4582b lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -285,7 +285,7 @@ tool_dependency = tool_dependency_util.mark_tool_dependency_installed( app, tool_dependency ) return tool_dependency -def install_package( app, elem, tool_shed_repository, tool_dependencies=None ): +def install_package( app, elem, tool_shed_repository, tool_dependencies=None, from_install_manager=False ): # The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository. sa_session = app.install_model.context tool_dependency = None @@ -317,14 +317,16 @@ tool_dependency_version=package_version ) can_install_tool_dependency = True if os.path.exists( install_dir ): - # Notice that we'll throw away the following tool_dependency if it can be installed. - tool_dependency, can_install_tool_dependency = \ - tool_dependency_util.sync_database_with_file_system( app, - tool_shed_repository, - package_name, - package_version, - install_dir, - tool_dependency_type='package' ) + if not from_install_manager: + # Notice that we'll throw away the following tool_dependency if it can be installed. + print 'Calling sync_database_with_file_system 2' + tool_dependency, can_install_tool_dependency = \ + tool_dependency_util.sync_database_with_file_system( app, + tool_shed_repository, + package_name, + package_version, + install_dir, + tool_dependency_type='package' ) else: can_install_tool_dependency = True if can_install_tool_dependency: diff -r cce4687a7ccc56a47db95498b0ae86f0f5986125 -r 9b337a87d6eca3bf9f7448d49337d231e3b4582b lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -435,7 +435,7 @@ all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts return all_required_repo_info_dict -def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_config, tool_dependencies ): +def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_config, tool_dependencies, from_install_manager=False ): """ Install and build tool dependencies defined in the tool_dependencies_config. This config's tag sets can currently refer to installation methods in Galaxy's tool_dependencies module. In the future, proprietary fabric scripts contained in the repository will be supported. @@ -487,7 +487,11 @@ error_message=None, remove_from_disk=False ) else: - tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) + tool_dependency = install_package( app, + elem, + tool_shed_repository, + tool_dependencies=tool_dependencies, + from_install_manager=from_install_manager ) except Exception, e: error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) ) log.exception( error_message ) diff -r cce4687a7ccc56a47db95498b0ae86f0f5986125 -r 9b337a87d6eca3bf9f7448d49337d231e3b4582b lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -91,9 +91,9 @@ file_path = elem.get( 'file', None ) if file_path: path, name = os.path.split( file_path ) - if name in migrated_tool_configs_dict: - tool_dependencies = migrated_tool_configs_dict[ name ] - missing_tool_configs_dict[ name ] = tool_dependencies + for migrated_tool_config in migrated_tool_configs_dict.keys(): + if migrated_tool_config in [ file_path, name ]: + missing_tool_configs_dict[ name ] = migrated_tool_configs_dict[ migrated_tool_config ] return missing_tool_configs_dict def get_non_shed_tool_panel_configs( app ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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