A couple bugfixes and a multi-update for datasets in the admin-side browser.

lib/galaxy/web/controllers/admin.py

@@ -563,8 +563,8 @@ class Admin( BaseController ):
         params = util.Params( kwd )
         if 'new' in kwd:
             if params.new == 'submitted':
-                library = trans.app.model.Library( name = params.name, description = params.description )
-                root_folder = trans.app.model.LibraryFolder( name = params.name, description = "" )
+                library = trans.app.model.Library( name = util.restore_text( params.name ), description = util.restore_text( params.description ) )
+                root_folder = trans.app.model.LibraryFolder( name = util.restore_text( params.name ), description = "" )
                 root_folder.flush()
                 library.root_folder = root_folder
                 library.flush()
@@ -578,10 +578,10 @@ class Admin( BaseController ):
             if params.rename == 'submitted':
                 if 'root_folder' in kwd:
                     root_folder = library.root_folder
-                    root_folder.name = params.name
+                    root_folder.name = util.restore_text( params.name )
                     root_folder.flush()
-                library.name = params.name
-                library.description = params.description
+                library.name = util.restore_text( params.name )
+                library.description = util.restore_text( params.description )
                 library.flush()
                 return trans.response.send_redirect( web.url_for( action='library_browser' ) )
             return trans.show_form( 
@@ -616,7 +616,7 @@ class Admin( BaseController ):
         folder = trans.app.model.LibraryFolder.get( id )
         if 'new' in kwd:
             if params.new == 'submitted':
-                new_folder = trans.app.model.LibraryFolder( name = params.name, description = params.description )
+                new_folder = trans.app.model.LibraryFolder( name = util.restore_text( params.name ), description = util.restore_text( params.description ) )
                 # We are associating the last used genome_build with folders, so we will always
                 # initialize a new folder with the first dbkey in util.dbnames which is currently
                 # ?    unspecified (?)
@@ -632,8 +632,8 @@ class Admin( BaseController ):
                     .add_input( 'hidden', '', 'id', id, use_label = False  ) )
         elif 'rename' in kwd:
             if params.rename == 'submitted':
-                folder.name = params.name
-                folder.description = params.description
+                folder.name = util.restore_text( params.name )
+                folder.description = util.restore_text( params.description )
                 folder.flush()
                 return trans.response.send_redirect( web.url_for( action='library_browser' ) )
             return trans.show_form( 
@@ -908,6 +908,7 @@ class Admin( BaseController ):
                     else:
                         setattr(dataset.metadata,name,spec.unwrap(p.get(name, None), p))
     
+                dataset.metadata.dbkey = dbkey
                 dataset.datatype.after_edit( dataset )
                 trans.app.model.flush()
                 return trans.show_ok_message( "Attributes updated" )
@@ -1039,6 +1040,27 @@ class Admin( BaseController ):
         else:
             trans.response.send_redirect( web.url_for( action='library_browser' ) )
     @web.expose
+    def datasets( self, trans, **kwd ):
+        if not self.user_is_admin( trans ):
+            return trans.show_error_message( no_privilege_msg )
+        params = util.Params( kwd )
+        if 'with-selected' in kwd:
+            if not params.dataset_ids:
+                return trans.show_error_message( "At least one dataset must be selected." )
+            dataset_ids = listify( params.dataset_ids )
+            if params.action == 'edit':
+                trans.response.send_redirect( web.url_for( action = 'dataset', id = ",".join( dataset_ids ) ) )
+            elif params.action == 'delete':
+                for id in dataset_ids:
+                    d = trans.app.model.LibraryFolderDatasetAssociation.get( id )
+                    d.deleted = True
+                    d.flush()
+                trans.response.send_redirect( web.url_for( action = 'library_browser' ) )
+            else:
+                return trans.show_error_message( "Not implemented." )
+        else:
+            return trans.show_error_message( "Galaxy can't operate on datasets without an operation." )
+    @web.expose
     def delete_dataset( self, trans, id=None, **kwd):
         if not self.user_is_admin( trans ):
             return trans.show_error_message( no_privilege_msg )

templates/admin/library/browser.mako

@@ -56,6 +56,15 @@
             });
         });
     });
+    function checkForm() {
+        if ( $("select#with-selected-select option:selected").text() == "delete" ) {
+            if ( confirm( "Are you sure you want to delete these datasets?" ) ) {
+                return true;
+            } else {
+                return false;
+            }
+        }
+    }
 </script>
 
 <%def name="render_folder( parent, parent_pad )">
@@ -130,7 +139,7 @@
         </a>
     </li>
 </ul>
-<form name="import_from_library" action="${h.url_for( '/library/import_datasets' )}" method="post">
+<form name="update_multiple_datasets" action="${h.url_for( action='datasets' )}" onSubmit="javascript:return checkForm();" method="post">
 <ul>
 %for library in libraries:
   ##%if trans.app.security_agent.check_folder_contents( trans.user, library ):
@@ -158,5 +167,13 @@
   ##%endif
 %endfor
 </ul>
-##<input type="submit" class="primary-button" name="import_dataset" value="Import selected datasets"/>
+<div style="float: right;">
+    With selected datasets:
+    <select name="action" id="with-selected-select">
+        <option value="None" selected></option>
+        <option value="edit">edit permissions</option>
+        <option value="delete">delete</option>
+    </select>
+    <input type="submit" class="primary-button" name="with-selected" id="with-selected-submit" value="go"/>
+</div>
 </form>

templates/admin/library/common.mako

@@ -192,7 +192,7 @@
             </%doc>
             <table cellspacing="0" cellpadding="0" border="0" width="100%"><tr>
 	    <td width="*">
-                <input type="checkbox" name="import_ids" value="${data.id}"/>
+                <input type="checkbox" name="dataset_ids" value="${data.id}"/>
                 <span class="historyItemTitle"><b>${data.display_name()}</b></span>
                 <a id="dataset-${data.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
                 <div popupmenu="dataset-${data.id}-popup">

templates/library/browser.mako

@@ -58,18 +58,52 @@
     });
 </script>
 
+<![if gte IE 7]>
+<script type="text/javascript">
+    q( document ).ready( function() {
+        // Add rollover effect to any image with a 'rollover' attribute
+        preload_images = {}
+        q( "img[@rollover]" ).each( function() {
+            var r = q(this).attr('rollover');
+            var s = q(this).attr('src');
+            preload_images[r] = true;
+            q(this).hover( 
+                function() { q(this).attr( 'src', r ) },
+                function() { q(this).attr( 'src', s ) }
+            )
+        })
+        for ( r in preload_images ) { q( "<img>" ).attr( "src", r ) }
+    })
+</script>
+<![endif]>
+
 <%def name="render_folder( parent, parent_pad )">
   <%
     if not trans.app.security_agent.check_folder_contents( trans.user, parent ):
       return ""
     pad = parent_pad + 20
+    if parent_pad == 0:
+        expander = "/static/images/silk/resultset_bottom.png"
+        folder = "/static/images/silk/folder_page.png"
+        subfolder = False
+    else:
+        expander = "/static/images/silk/resultset_next.png"
+        folder = "/static/images/silk/folder.png"
+        subfolder = True
   %>
-  %if parent_pad == 0:
-    <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;"><div class="rowTitle"><img src="${h.url_for( '/static/images/silk/resultset_bottom.png' )}" class="expanderIcon"/><img src="${h.url_for( '/static/images/silk/folder_page.png' )}" class="rowIcon"/> ${parent.name}</div></li>
-    <ul>
-  %else:
-    <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;"><div class="rowTitle"><img src="${h.url_for( '/static/images/silk/resultset_next.png' )}" class="expanderIcon"/><img src="${h.url_for( '/static/images/silk/folder.png' )}" class="rowIcon"/> ${parent.name}</div></li>
+  <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;">
+    <div class="rowTitle">
+      <img src="${h.url_for( expander )}" class="expanderIcon"/><img src="${h.url_for( folder )}" class="rowIcon"/>
+      ${parent.name}
+      %if parent.description:
+        <i>- ${parent.description}</i>
+      %endif
+    </div>
+  </li>
+  %if subfolder:
     <ul id="subFolder">
+  %else:
+    <ul>
   %endif
       %for folder in parent.active_folders:
         ${render_folder( folder, pad )}
@@ -88,7 +122,13 @@
 %for library in libraries:
   %if trans.app.security_agent.check_folder_contents( trans.user, library ):
   <li class="libraryRow libraryOrFolderRow" id="libraryRow"><div class="rowTitle"><table cellspacing="0" cellpadding="0" border="0" width="100%" class="libraryTitle"><tr>
-    <th width="*"><img src="${h.url_for( '/static/images/silk/resultset_bottom.png' )}" class="expanderIcon"/><img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/> ${library.name}</th>
+    <th width="*">
+        <img src="${h.url_for( '/static/images/silk/resultset_bottom.png' )}" class="expanderIcon"/><img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/>
+        ${library.name}
+        %if library.description:
+          <i>- ${library.description}</i>
+        %endif
+    </th>
     <th width="100">Format</th>
     <th width="50">Db</th>
     <th width="200">Info</th>

templates/library/common.mako

@@ -38,7 +38,18 @@
 	    </div>
             </%doc>
             <table cellspacing="0" cellpadding="0" border="0" width="100%"><tr>
-	    <td width="*"><input type="checkbox" name="import_ids" value="${data.id}"/> <span class="historyItemTitle"><b>${data.display_name()}</b></span></td>
+	    <td width="*">
+              <div style="float: right; padding-right: 2px;">
+                <a href="${h.url_for( controller='root', action='edit', lid=data.id )}">
+                  <img src="${h.url_for('/static/images/pencil_icon.png')}" 
+                    rollover="${h.url_for('/static/images/pencil_icon_dark.png')}" 
+                    width='16' height='16' alt='view or edit attributes' title='view or edit attributes'
+                    class='editButton' style='vertical-align: middle' border='0'>
+                </a>
+              </div>
+              <input type="checkbox" name="import_ids" value="${data.id}"/>
+              <span class="historyItemTitle"><b>${data.display_name()}</b></span>
+            </td>
             <td width="100">${data.ext}</td>
             <td width="50"><span class="${data.dbkey}">${data.dbkey}</span></td>
             <td width="200">${data.info}</td>
@@ -50,18 +61,7 @@
         <div id="info${data.id}" class="historyItemBody">
             %if not trans.app.security_agent.allow_action( trans.user, data.permitted_actions.DATASET_ACCESS, dataset = data.dataset ):
                 <div>You do not have permission to view this dataset.</div>
-            %elif data_state == "queued":
-                <div>Job is waiting to run</div>
-            %elif data_state == "running":
-                <div>Job is currently running</div>
-            %elif data_state == "error":
-                <div>
-                    An error occurred running this job: <i>${data.display_info().strip()}</i>, 
-                    <a href="${h.url_for( controller='dataset', action='errors', id=data.id )}" target="galaxy_main">report this error</a>
-                </div>
-            %elif data_state == "empty":
-                <div>No data: <i>${data.display_info()}</i></div>
-            %elif data_state == "ok":
+            %else:
                 <div>
                     ${data.blurb}
                 </div>
@@ -82,8 +82,6 @@
                 %if data.peek != "no peek":
                     <div><pre id="peek${data.id}" class="peek">${data.display_peek()}</pre></div>
                 %endif
-	    %else:
-		<div>Error: unknown dataset state "${data_state}".</div>
             %endif
             ## Recurse for child datasets
             %if len( data.children ) > 0: