[galaxy-dev] [hg] galaxy 3194: Data library cleanup

5 Jan 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/4743015d9a57
changeset: 3194:4743015d9a57
user:      Greg Von Kuster greg@bx.psu.edu
date:      Wed Dec 23 20:26:01 2009 -0500
description:
Data library cleanup
- move / merge all duplicate methods from the library_and library_admin controllers into the library_common controller
- move / merge all duplicate mako templates into the ~/library/common directory
- make the admin view library browser a grid
- all library item ids are now encoded
diffstat:
lib/galaxy/model/__init__.py                              |    14 +
 lib/galaxy/tools/actions/upload_common.py                 |     2 +-
 lib/galaxy/web/controllers/library.py                     |   944 ----------
 lib/galaxy/web/controllers/library_admin.py               |  1004 +----------
 lib/galaxy/web/controllers/library_common.py              |  1119 ++++++++++++-
 lib/galaxy/web/controllers/tool_runner.py                 |     2 +-
 templates/admin/library/browse_libraries.mako             |    51 -
 templates/admin/library/browse_library.mako               |   325 ---
 templates/admin/library/common.mako                       |    59 -
 templates/admin/library/folder_info.mako                  |    39 -
 templates/admin/library/folder_permissions.mako           |    22 -
 templates/admin/library/grid.mako                         |     1 +
 templates/admin/library/ldda_edit_info.mako               |   135 -
 templates/admin/library/ldda_info.mako                    |   110 -
 templates/admin/library/ldda_permissions.mako             |    64 -
 templates/admin/library/library_dataset_info.mako         |    50 -
 templates/admin/library/library_dataset_permissions.mako  |    28 -
 templates/admin/library/library_info.mako                 |    50 -
 templates/admin/library/library_permissions.mako          |    21 -
 templates/admin/library/new_folder.mako                   |    44 -
 templates/admin/library/new_library.mako                  |     2 +-
 templates/admin/library/upload.mako                       |    50 -
 templates/admin/requests/show_request.mako                |     2 +-
 templates/base_panels.mako                                |     4 +-
 templates/library/browse_libraries.mako                   |     2 +-
 templates/library/browse_library.mako                     |   388 ----
 templates/library/common.mako                             |    59 -
 templates/library/common/browse_library.mako              |   441 +++++
 templates/library/common/common.mako                      |   370 ++++
 templates/library/common/folder_info.mako                 |    56 +
 templates/library/common/folder_permissions.mako          |    20 +
 templates/library/common/ldda_edit_info.mako              |   171 +
 templates/library/common/ldda_info.mako                   |   114 +
 templates/library/common/ldda_permissions.mako            |    65 +
 templates/library/common/library_dataset_info.mako        |    71 +
 templates/library/common/library_dataset_permissions.mako |    34 +
 templates/library/common/library_info.mako                |    61 +
 templates/library/common/library_item_info.mako           |    15 +
 templates/library/common/library_permissions.mako         |    28 +
 templates/library/common/new_folder.mako                  |    44 +
 templates/library/common/select_info_template.mako        |    44 +
 templates/library/common/upload.mako                      |    56 +
 templates/library/folder_info.mako                        |    53 -
 templates/library/folder_permissions.mako                 |    20 -
 templates/library/ldda_edit_info.mako                     |   168 -
 templates/library/ldda_info.mako                          |   112 -
 templates/library/ldda_permissions.mako                   |    64 -
 templates/library/library_dataset_common.mako             |   265 ---
 templates/library/library_dataset_info.mako               |    68 -
 templates/library/library_dataset_permissions.mako        |    31 -
 templates/library/library_info.mako                       |    64 -
 templates/library/library_item_info.mako                  |    15 -
 templates/library/library_permissions.mako                |    25 -
 templates/library/new_folder.mako                         |    44 -
 templates/library/select_info_template.mako               |    44 -
 templates/library/upload.mako                             |    47 -
 templates/mobile/manage_library.mako                      |    16 +-
 templates/requests/show_request.mako                      |     9 +-
 test/base/twilltestcase.py                                |   109 +-
 test/functional/test_forms_and_requests.py                |    14 +-
 test/functional/test_security_and_libraries.py            |   416 +++-
 61 files changed, 3147 insertions(+), 4618 deletions(-)
diffs (truncated from 9178 to 3000 lines):
diff -r 9f966847abda -r 4743015d9a57 lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py	Tue Dec 22 18:49:34 2009 -0500
+++ b/lib/galaxy/model/__init__.py	Wed Dec 23 20:26:01 2009 -0500
@@ -746,6 +746,13 @@
                     return template.get_widgets( trans.user, contents=info.content )
             return template.get_widgets( trans.user )
         return []
+    def get_display_name( self ):
+        # Library name can be either a string or a unicode object. If string, 
+        # convert to unicode object assuming 'utf-8' format.
+        name = self.name
+        if isinstance( name, str ):
+            name = unicode( name, 'utf-8' )
+        return name
class LibraryFolder( object ):
     def __init__( self, name=None, description=None, item_count=0, order_id=None ):
@@ -811,6 +818,13 @@
     def active_datasets( self ):
          # This needs to be a list
         return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ]
+    def get_display_name( self ):
+        # Library folder name can be either a string or a unicode object. If string, 
+        # convert to unicode object assuming 'utf-8' format.
+        name = self.name
+        if isinstance( name, str ):
+            name = unicode( name, 'utf-8' )
+        return name
class LibraryDataset( object ):
     # This class acts as a proxy to the currently selected LDDA
diff -r 9f966847abda -r 4743015d9a57 lib/galaxy/tools/actions/upload_common.py
--- a/lib/galaxy/tools/actions/upload_common.py	Tue Dec 22 18:49:34 2009 -0500
+++ b/lib/galaxy/tools/actions/upload_common.py	Wed Dec 23 20:26:01 2009 -0500
@@ -41,7 +41,7 @@
     # See if we have any template field contents
     library_bunch.template_field_contents = []
     template_id = params.get( 'template_id', None )
-    library_bunch.folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder_id )
+    library_bunch.folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
     # We are inheriting the folder's info_association, so we did not
     # receive any inherited contents, but we may have redirected here
     # after the user entered template contents ( due to errors ).
diff -r 9f966847abda -r 4743015d9a57 lib/galaxy/web/controllers/library.py
--- a/lib/galaxy/web/controllers/library.py	Tue Dec 22 18:49:34 2009 -0500
+++ b/lib/galaxy/web/controllers/library.py	Wed Dec 23 20:26:01 2009 -0500
@@ -3,50 +3,9 @@
 from galaxy.datatypes import sniff
 from galaxy import util
 from galaxy.util.odict import odict
-from galaxy.util.streamball import StreamBall
-import logging, tempfile, zipfile, tarfile, os, sys
-
-if sys.version_info[:2] < ( 2, 6 ):
-    zipfile.BadZipFile = zipfile.error
-if sys.version_info[:2] < ( 2, 5 ):
-    zipfile.LargeZipFile = zipfile.error
log = logging.getLogger( __name__ )
-# Test for available compression types
-tmpd = tempfile.mkdtemp()
-comptypes = []
-for comptype in ( 'gz', 'bz2' ):
-    tmpf = os.path.join( tmpd, 'compression_test.tar.' + comptype )
-    try:
-        archive = tarfile.open( tmpf, 'w:' + comptype )
-        archive.close()
-        comptypes.append( comptype )
-    except tarfile.CompressionError:
-        log.exception( "Compression error when testing %s compression.  This option will be disabled for library downloads." % comptype )
-    try:
-        os.unlink( tmpf )
-    except OSError:
-        pass
-ziptype = '32'
-tmpf = os.path.join( tmpd, 'compression_test.zip' )
-try:
-    archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
-    archive.close()
-    comptypes.append( 'zip' )
-    ziptype = '64'
-except RuntimeError:
-    log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." )
-except (TypeError, zipfile.LargeZipFile):
-    # ZIP64 is only in Python2.5+.  Remove TypeError when 2.4 support is dropped
-    log.warning( 'Max zip file size is 2GB, ZIP64 not supported' )
-    comptypes.append( 'zip' )
-try:
-    os.unlink( tmpf )
-except OSError:
-    pass
-os.rmdir( tmpd )
-
 class Library( BaseController ):
     @web.expose
     def index( self, trans, **kwd ):
@@ -89,906 +48,3 @@
                                     default_action=params.get( 'default_action', None ),
                                     msg=msg,
                                     messagetype=messagetype )
-    @web.expose
-    def browse_library( self, trans, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        library_id = params.get( 'obj_id', None )
-        if not library_id:
-            # To handle bots
-            msg = "You must specify a library id."
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_libraries',
-                                                              default_action=params.get( 'default_action', None ),
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        library = trans.sa_session.query( trans.app.model.Library ).get( library_id )
-        if not library:
-            # To handle bots
-            msg = "Invalid library id ( %s )." % str( library_id )
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_libraries',
-                                                              default_action=params.get( 'default_action', None ),
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        created_ldda_ids = params.get( 'created_ldda_ids', '' )
-        hidden_folder_ids = util.listify( util.restore_text( params.get( 'hidden_folder_ids', '' ) ) )
-        if created_ldda_ids and not msg:
-            msg = "%d datasets are now uploading in the background to the library '%s' ( each is selected ).  "  % ( len( created_ldda_ids.split(',') ), library.name )
-            msg += "Do not navigate away from Galaxy or use the browser's "stop" or "reload" buttons ( on this tab ) until the upload(s) change from the "uploading" state."
-            messagetype = "info"
-        return trans.fill_template( '/library/browse_library.mako', 
-                                    library=library,
-                                    created_ldda_ids=created_ldda_ids,
-                                    hidden_folder_ids=hidden_folder_ids,
-                                    default_action=params.get( 'default_action', None ),
-                                    comptypes=comptypes,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    def library( self, trans, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        library_id = params.get( 'obj_id', None )
-        # TODO: eventually we'll want the ability for users to create libraries
-        if params.get( 'delete', False ):
-            action = 'delete'
-        elif params.get( 'permissions', False ):
-            action = 'permissions'
-        else:
-            action = 'information'
-        if not library_id:
-            msg = "You must specify a library."
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_libraries',
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        library = trans.sa_session.query( trans.app.model.Library ).get( int( library_id ) )
-        if not library:
-            msg = "Invalid library id ( %s ) specified." % str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_libraries',
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        if action == 'information':
-            # See if we have any associated templates
-            widgets = library.get_template_widgets( trans )
-            if params.get( 'rename_library_button', False ):
-                old_name = library.name
-                new_name = util.restore_text( params.name )
-                new_description = util.restore_text( params.description )
-                if not new_name:
-                    msg = 'Enter a valid name'
-                    return trans.fill_template( '/library/library_info.mako',
-                                                library=library,
-                                                widgets=widgets,
-                                                msg=msg,
-                                                messagetype='error' )
-                else:
-                    library.name = new_name
-                    library.description = new_description
-                    # Rename the root_folder
-                    library.root_folder.name = new_name
-                    library.root_folder.description = new_description
-                    trans.sa_session.add_all( ( library, library.root_folder ) )
-                    trans.sa_session.flush()
-                    msg = "Library '%s' has been renamed to '%s'" % ( old_name, new_name )
-                    return trans.response.send_redirect( web.url_for( controller='library',
-                                                                      action='library',
-                                                                      obj_id=library.id,
-                                                                      edit_info=True,
-                                                                      msg=util.sanitize_text( msg ),
-                                                                      messagetype='done' ) )
-            return trans.fill_template( '/library/library_info.mako',
-                                        library=library,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif action == 'permissions':
-            if params.get( 'update_roles_button', False ):
-                # The user clicked the Save button on the 'Associate With Roles' form
-                permissions = {}
-                for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
-                    permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-                trans.app.security_agent.set_all_library_permissions( library, permissions )
-                trans.sa_session.refresh( library )
-                # Copy the permissions to the root folder
-                trans.app.security_agent.copy_library_permissions( library, library.root_folder )
-                msg = "Permissions updated for library '%s'" % library.name
-                return trans.response.send_redirect( web.url_for( controller='library',
-                                                                  action='library',
-                                                                  obj_id=library.id,
-                                                                  permissions=True,
-                                                                  msg=util.sanitize_text( msg ),
-                                                                  messagetype='done' ) )
-            return trans.fill_template( '/library/library_permissions.mako',
-                                        library=library,
-                                        msg=msg,
-                                        messagetype=messagetype )
-    @web.expose
-    def folder( self, trans, obj_id, library_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        if params.get( 'new', False ):
-            action = 'new'
-        elif params.get( 'delete', False ):
-            action = 'delete'
-        elif params.get( 'permissions', False ):
-            action = 'permissions'
-        else:
-            # 'information' will be the default
-            action = 'information'
-        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( obj_id ) )
-        if not folder:
-            msg = "Invalid folder specified, id: %s" % str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        user, roles = trans.get_user_and_roles()
-        if action == 'new':
-            if params.new == 'submitted':
-                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 (?)
-                new_folder.genome_build = util.dbnames.default_value
-                folder.add_folder( new_folder )
-                trans.sa_session.add( new_folder )
-                trans.sa_session.flush()
-                # New folders default to having the same permissions as their parent folder
-                trans.app.security_agent.copy_library_permissions( folder, new_folder )
-                msg = "New folder named '%s' has been added to the library" % new_folder.name
-                return trans.response.send_redirect( web.url_for( controller='library',
-                                                                  action='browse_library',
-                                                                  obj_id=library_id,
-                                                                  msg=util.sanitize_text( msg ),
-                                                                  messagetype='done' ) )
-            return trans.fill_template( '/library/new_folder.mako',
-                                        library_id=library_id,
-                                        folder=folder,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif action == 'information':
-            # See if we have any associated templates
-            widgets = folder.get_template_widgets( trans )
-            if params.get( 'rename_folder_button', False ):
-                if trans.app.security_agent.can_modify_library_item( user, roles, folder ):
-                    old_name = folder.name
-                    new_name = util.restore_text( params.name )
-                    new_description = util.restore_text( params.description )
-                    if not new_name:
-                        msg = 'Enter a valid name'
-                        return trans.fill_template( "/library/folder_info.mako",
-                                                    folder=folder,
-                                                    library_id=library_id,
-                                                    widgets=widgets,
-                                                    msg=msg,
-                                                    messagetype='error' )
-                    else:
-                        folder.name = new_name
-                        folder.description = new_description
-                        trans.sa_session.add( folder )
-                        trans.sa_session.flush()
-                        msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name )
-                        return trans.response.send_redirect( web.url_for( controller='library',
-                                                                          action='folder',
-                                                                          obj_id=folder.id,
-                                                                          library_id=library_id,
-                                                                          rename=True,
-                                                                          msg=util.sanitize_text( msg ),
-                                                                          messagetype='done' ) )
-                else:
-                    msg = "You are not authorized to edit this folder"
-                    return trans.fill_template( "/library/folder_info.mako",
-                                                folder=folder,
-                                                library_id=library_id,
-                                                widgets=widgets,
-                                                msg=msg,
-                                                messagetype='error' )
-            return trans.fill_template( '/library/folder_info.mako',
-                                        folder=folder,
-                                        library_id=library_id,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif action == 'permissions':
-            if params.get( 'update_roles_button', False ):
-                # The user clicked the Save button on the 'Associate With Roles' form
-                if trans.app.security_agent.can_manage_library_item( user, roles, folder ):
-                    permissions = {}
-                    for k, v in trans.app.model.Library.permitted_actions.items():
-                        in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ]
-                        permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-                    trans.app.security_agent.set_all_library_permissions( folder, permissions )
-                    trans.sa_session.refresh( folder )
-                    msg = 'Permissions updated for folder %s' % folder.name
-                    return trans.response.send_redirect( web.url_for( controller='library',
-                                                                      action='folder',
-                                                                      obj_id=folder.id,
-                                                                      library_id=library_id,
-                                                                      permissions=True,
-                                                                      msg=util.sanitize_text( msg ),
-                                                                      messagetype='done' ) )
-                else:
-                    msg = "You are not authorized to manage permissions on this folder"
-                    return trans.response.send_redirect( web.url_for( controller='library',
-                                                                      action='folder',
-                                                                      obj_id=folder.id,
-                                                                      library_id=library_id,
-                                                                      permissions=True,
-                                                                      msg=util.sanitize_text( msg ),
-                                                                      messagetype='error' ) )
-            return trans.fill_template( '/library/folder_permissions.mako',
-                                        folder=folder,
-                                        library_id=library_id,
-                                        msg=msg,
-                                        messagetype=messagetype )
-    @web.expose
-    def library_dataset( self, trans, obj_id, library_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        if params.get( 'permissions', False ):
-            action = 'permissions'
-        else:
-            action = 'information'
-        library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( obj_id )
-        if not library_dataset:
-            msg = "Invalid library dataset specified, id: %s" %str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        user, roles = trans.get_user_and_roles()
-        if action == 'information':
-            if params.get( 'edit_attributes_button', False ):
-                if trans.app.security_agent.can_modify_library_item( user, roles, library_dataset ):
-                    if params.get( 'edit_attributes_button', False ):
-                        old_name = library_dataset.name
-                        new_name = util.restore_text( params.get( 'name', '' ) )
-                        new_info = util.restore_text( params.get( 'info', '' ) )
-                        if not new_name:
-                            msg = 'Enter a valid name'
-                            messagetype = 'error'
-                        else:
-                            library_dataset.name = new_name
-                            library_dataset.info = new_info
-                            trans.sa_session.add( library_dataset )
-                            trans.sa_session.flush()
-                            msg = "Dataset '%s' has been renamed to '%s'" % ( old_name, new_name )
-                            messagetype = 'done'
-                else:
-                    msg = "You are not authorized to change the attributes of this dataset"
-                    messagetype = "error"
-            return trans.fill_template( '/library/library_dataset_info.mako',
-                                        library_dataset=library_dataset,
-                                        library_id=library_id,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif action == 'permissions':
-            if params.get( 'update_roles_button', False ):
-                if trans.app.security_agent.can_manage_library_item( user, roles, library_dataset ):
-                    # The user clicked the Save button on the 'Associate With Roles' form
-                    permissions = {}
-                    for k, v in trans.app.model.Library.permitted_actions.items():
-                        in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
-                        permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-                    # Set the LIBRARY permissions on the LibraryDataset
-                    # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
-                    trans.app.security_agent.set_all_library_permissions( library_dataset, permissions )
-                    trans.sa_session.refresh( library_dataset )
-                    # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
-                    trans.app.security_agent.set_all_library_permissions( library_dataset.library_dataset_dataset_association, permissions )
-                    trans.sa_session.refresh( library_dataset.library_dataset_dataset_association )
-                    msg = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name
-                    messagetype = 'done'
-                else:
-                    msg = "You are not authorized to managed the permissions of this dataset"
-                    messagetype = "error"
-                return trans.fill_template( '/library/library_dataset_permissions.mako',
-                                            library_dataset=library_dataset,
-                                            library_id=library_id,
-                                            msg=msg,
-                                            messagetype=messagetype )
-    @web.expose
-    def ldda_edit_info( self, trans, library_id, folder_id, obj_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
-        if not ldda:
-            msg = "Invalid LibraryDatasetDatasetAssociation specified, obj_id: %s" % str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        dbkey = params.get( 'dbkey', '?' )
-        if isinstance( dbkey, list ):
-            dbkey = dbkey[0]
-        user, roles = trans.get_user_and_roles()
-        file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
-        file_formats.sort()
-        # See if we have any associated templates
-        widgets = ldda.get_template_widgets( trans )
-        if params.get( 'change', False ):
-            # The user clicked the Save button on the 'Change data type' form
-            if trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
-                if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
-                    trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
-                    trans.sa_session.flush()
-                    msg = "Data type changed for library dataset '%s'" % ldda.name
-                    messagetype = 'done'
-                else:
-                    msg = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype )
-                    messagetype = 'error'
-            else:
-                msg = "You are not authorized to change the data type of dataset '%s'" % ldda.name
-                messagetype = 'error'
-            return trans.fill_template( "/library/ldda_edit_info.mako", 
-                                        ldda=ldda,
-                                        library_id=library_id,
-                                        file_formats=file_formats,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif params.get( 'save', False ):
-            # The user clicked the Save button on the 'Edit Attributes' form
-            if trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
-                old_name = ldda.name
-                new_name = util.restore_text( params.get( 'name', '' ) )
-                new_info = util.restore_text( params.get( 'info', '' ) )
-                new_message = util.restore_text( params.get( 'message', '' ) )
-                if not new_name:
-                    msg = 'Enter a valid name'
-                    messagetype = 'error'
-                else:
-                    ldda.name = new_name
-                    ldda.info = new_info
-                    ldda.message = new_message
-                    # The following for loop will save all metadata_spec items
-                    for name, spec in ldda.datatype.metadata_spec.items():
-                        if spec.get("readonly"):
-                            continue
-                        optional = params.get( "is_" + name, None )
-                        if optional and optional == 'true':
-                            # optional element... == 'true' actually means it is NOT checked (and therefore ommitted)
-                            setattr( ldda.metadata, name, None )
-                        else:
-                            setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) )
-                    ldda.metadata.dbkey = dbkey
-                    ldda.datatype.after_setting_metadata( ldda )
-                    trans.sa_session.flush()
-                    msg = 'Attributes updated for library dataset %s' % ldda.name
-                    messagetype = 'done'
-            else:
-                msg = "you are not authorized to edit the attributes of dataset '%s'" % ldda.name
-                messagetype = 'error'
-            return trans.fill_template( "/library/ldda_edit_info.mako", 
-                                        ldda=ldda,
-                                        library_id=library_id,
-                                        file_formats=file_formats,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif params.get( 'detect', False ):
-            # The user clicked the Auto-detect button on the 'Edit Attributes' form
-            if trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
-                for name, spec in ldda.datatype.metadata_spec.items():
-                    # We need to be careful about the attributes we are resetting
-                    if name not in [ 'name', 'info', 'dbkey' ]:
-                        if spec.get( 'default' ):
-                            setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) )
-                ldda.datatype.set_meta( ldda )
-                ldda.datatype.after_setting_metadata( ldda )
-                trans.sa_session.flush()
-                msg = 'Attributes updated for library dataset %s' % ldda.name
-                messagetype = 'done'
-            else:
-                msg = "you are not authorized to edit the attributes of dataset '%s'" % ldda.name
-                messagetype = 'error'
-            return trans.fill_template( "/library/ldda_edit_info.mako", 
-                                        ldda=ldda,
-                                        library_id=library_id,
-                                        file_formats=file_formats,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif params.get( 'delete', False ):
-            if trans.app.security_agent.can_modify_library_item( user, roles, folder ):
-                ldda.deleted = True
-                trans.sa_session.add( ldda )
-                trans.sa_session.flush()
-                msg = 'Dataset %s has been removed from this data library' % ldda.name
-                messagetype = 'done'
-            else:
-                msg = "you are not authorized to delete dataset '%s'" % ldda.name
-                messagetype = 'error'
-            return trans.fill_template( "/library/ldda_edit_info.mako", 
-                                        ldda=ldda,
-                                        library_id=library_id,
-                                        file_formats=file_formats,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        if trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
-            if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey:
-                # Copy dbkey into metadata, for backwards compatability
-                # This looks like it does nothing, but getting the dbkey
-                # returns the metadata dbkey unless it is None, in which
-                # case it resorts to the old dbkey.  Setting the dbkey
-                # sets it properly in the metadata
-                ldda.metadata.dbkey = ldda.dbkey
-        return trans.fill_template( "/library/ldda_edit_info.mako", 
-                                    ldda=ldda,
-                                    library_id=library_id,
-                                    file_formats=file_formats,
-                                    widgets=widgets,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    def ldda_display_info( self, trans, library_id, folder_id, obj_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
-        if not ldda:
-            msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller='admin',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        # See if we have any associated templates
-        widgets = ldda.get_template_widgets( trans )
-        return trans.fill_template( '/library/ldda_info.mako',
-                                    ldda=ldda,
-                                    library_id=library_id,
-                                    widgets=widgets,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    def ldda_manage_permissions( self, trans, library_id, folder_id, obj_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        obj_ids = util.listify( obj_id )
-        # Display permission form, permissions will be updated for all lddas simultaneously.
-        lddas = []
-        for obj_id in [ int( obj_id ) for obj_id in obj_ids ]:
-            ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
-            if ldda is None:
-                msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( obj_id )
-                trans.response.send_redirect( web.url_for( controller='library',
-                                                           action='browse_library',
-                                                           obj_id=library_id,
-                                                           msg=util.sanitize_text( msg ),
-                                                           messagetype='error' ) )
-            lddas.append( ldda )
-        if params.get( 'update_roles_button', False ):
-            if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \
-                trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ):
-                permissions = {}
-                for k, v in trans.app.model.Dataset.permitted_actions.items():
-                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
-                    permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-                for ldda in lddas:
-                    # Set the DATASET permissions on the Dataset
-                    trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions )
-                    trans.sa_session.refresh( ldda.dataset )
-                permissions = {}
-                for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
-                    permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-                for ldda in lddas:
-                    # Set the LIBRARY permissions on the LibraryDataset
-                    # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
-                    trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions )
-                    trans.sa_session.refresh( ldda.library_dataset )
-                    # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
-                    trans.app.security_agent.set_all_library_permissions( ldda, permissions )
-                    trans.sa_session.refresh( ldda )
-                msg = 'Permissions and roles have been updated on %d datasets' % len( lddas )
-                messagetype = 'done'
-            else:
-                msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name
-                messagetype = 'error'
-            return trans.fill_template( "/library/ldda_permissions.mako",
-                                        ldda=lddas,
-                                        library_id=library_id,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \
-            trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ):
-            # Ensure that the permissions across all library items are identical, otherwise we can't update them together.
-            check_list = []
-            for ldda in lddas:
-                permissions = []
-                # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation
-                # will always be the same as the permissions on the associated LibraryDataset, so we only need to
-                # check one Library object
-                for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ):
-                    if library_permission.action not in permissions:
-                        permissions.append( library_permission.action )
-                for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ):
-                    if dataset_permission.action not in permissions:
-                        permissions.append( dataset_permission.action )
-                permissions.sort()
-                if not check_list:
-                    check_list = permissions
-                if permissions != check_list:
-                    msg = 'The datasets you selected do not have identical permissions, so they can not be updated together'
-                    trans.response.send_redirect( web.url_for( controller='library',
-                                                               action='browse_library',
-                                                               obj_id=library_id,
-                                                               msg=util.sanitize_text( msg ),
-                                                               messagetype='error' ) )
-        else:
-            msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name
-            messagetype = 'error'
-        return trans.fill_template( "/library/ldda_permissions.mako",
-                                    ldda=lddas,
-                                    library_id=library_id,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    def upload_library_dataset( self, trans, library_id, folder_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        dbkey = params.get( 'dbkey', None )
-        if isinstance( dbkey, list ):
-            last_used_build = dbkey[0]
-        else:
-            last_used_build = dbkey
-        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder_id )
-        if folder and last_used_build in [ 'None', None, '?' ]:
-            last_used_build = folder.genome_build
-        replace_id = params.get( 'replace_id', None )
-        if replace_id not in [ None, 'None' ]:
-            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( replace_id )
-            if not last_used_build:
-                last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
-            # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
-            upload_option = 'upload_file'
-        else:
-            replace_dataset = None
-            upload_option = params.get( 'upload_option', 'upload_file' )
-        user, roles = trans.get_user_and_roles()
-        if trans.app.security_agent.can_add_library_item( user, roles, folder ) or \
-             ( replace_dataset and trans.app.security_agent.can_modify_library_item( user, roles, replace_dataset ) ):
-            if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ):
-                # See if we have any inherited templates, but do not inherit contents.
-                info_association, inherited = folder.get_info_association( inherited=True )
-                if info_association:
-                    template_id = str( info_association.template.id )
-                    widgets = folder.get_template_widgets( trans, get_contents=False )
-                else:
-                    template_id = 'None'
-                    widgets = []
-                created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans,
-                                                                                               controller='library', 
-                                                                                               library_id=library_id,
-                                                                                               folder_id=folder_id,
-                                                                                               template_id=template_id,
-                                                                                               widgets=widgets,
-                                                                                               replace_dataset=replace_dataset,
-                                                                                               **kwd )
-                if created_outputs:
-                    ldda_id_list = [ str( v.id ) for v in created_outputs.values() ]
-                    total_added = len( created_outputs.values() )
-                    if replace_dataset:
-                        msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name )
-                    else:
-                        if not folder.parent:
-                            # Libraries have the same name as their root_folder
-                            msg = "Added %d datasets to the library '%s' ( each is selected ).  " % ( total_added, folder.name )
-                        else:
-                            msg = "Added %d datasets to the folder '%s' ( each is selected ).  " % ( total_added, folder.name )
-                    # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need
-                    # to check one of them to see if the current user can manage permissions on them.
-                    check_ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id_list[0] )
-                    if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ):
-                        if replace_dataset:
-                            default_action = ''
-                        else:
-                            msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
-                            default_action = 'manage_permissions'
-                    else:
-                        default_action = 'add'
-                    trans.response.send_redirect( web.url_for( controller='library',
-                                                               action='browse_library',
-                                                               obj_id=library_id,
-                                                               default_action=default_action,
-                                                               created_ldda_ids=",".join( ldda_id_list ), 
-                                                               msg=util.sanitize_text( msg ), 
-                                                               messagetype='done' ) )
-                    
-                else:
-                    msg = "Upload failed"
-                    trans.response.send_redirect( web.url_for( controller='library',
-                                                               action='browse_library',
-                                                               obj_id=library_id,
-                                                               created_ldda_ids=",".join( ldda_id_list ), 
-                                                               msg=util.sanitize_text( msg ), 
-                                                               messagetype='error' ) )
-        # See if we have any inherited templates, but do not inherit contents.
-        widgets = folder.get_template_widgets( trans, get_contents=False )
-        upload_option = params.get( 'upload_option', 'upload_file' )
-        # No dataset(s) specified, so display the upload form.  Send list of data formats to the form
-        # so the "extension" select list can be populated dynamically
-        file_formats = trans.app.datatypes_registry.upload_file_formats
-        # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
-        def get_dbkey_options( last_used_build ):
-            for dbkey, build_name in util.dbnames:
-                yield build_name, dbkey, ( dbkey==last_used_build )
-        dbkeys = get_dbkey_options( last_used_build )
-        # Send list of roles to the form so the dataset can be associated with 1 or more of them.
-        roles = trans.sa_session.query( trans.app.model.Role ) \
-                                .filter( trans.app.model.Role.table.c.deleted==False ) \
-                                .order_by( trans.app.model.Role.table.c.name )
-        # Send the current history to the form to enable importing datasets from history to library
-        history = trans.get_history()
-        trans.sa_session.refresh( history )
-        # If we're using nginx upload, override the form action
-        action = web.url_for( controller='library', action='upload_library_dataset' )
-        if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
-            action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action
-        return trans.fill_template( '/library/upload.mako',
-                                    upload_option=upload_option,
-                                    action=action,
-                                    library_id=library_id,
-                                    folder_id=folder_id,
-                                    replace_dataset=replace_dataset,
-                                    file_formats=file_formats,
-                                    dbkeys=dbkeys,
-                                    last_used_build=last_used_build,
-                                    roles=roles,
-                                    history=history,
-                                    widgets=widgets,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    def add_history_datasets_to_library( self, trans, library_id, folder_id, hda_ids='', **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        try:
-            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( folder_id ) )
-        except:
-            msg = "Invalid folder id: %s" % str( folder_id )
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        replace_id = params.get( 'replace_id', None )
-        if replace_id:
-            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( replace_id )
-        else:
-            replace_dataset = None
-        # See if the current history is empty
-        history = trans.get_history()
-        trans.sa_session.refresh( history )
-        if not history.active_datasets:
-            msg = 'Your current history is empty'
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        if params.get( 'add_history_datasets_to_library_button', False ):
-            hda_ids = util.listify( hda_ids )
-            if hda_ids:
-                dataset_names = []
-                created_ldda_ids = ''
-                for hda_id in hda_ids:
-                    hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( hda_id )
-                    if hda:
-                        ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset )
-                        created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) )
-                        dataset_names.append( ldda.name )
-                        if not replace_dataset:
-                            # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new 
-                            # LDDA and LibraryDataset.
-                            trans.app.security_agent.copy_library_permissions( folder, ldda )
-                            trans.app.security_agent.copy_library_permissions( folder, ldda.library_dataset )
-                        # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
-                        trans.app.security_agent.copy_library_permissions( ldda.library_dataset, ldda )
-                    else:
-                        msg = "The requested HistoryDatasetAssociation id %s is invalid" % str( hda_id )
-                        return trans.response.send_redirect( web.url_for( controller='library',
-                                                                          action='browse_library',
-                                                                          obj_id=library_id,
-                                                                          msg=util.sanitize_text( msg ), 
-                                                                          messagetype='error' ) )
-                if created_ldda_ids:
-                    created_ldda_ids = created_ldda_ids.lstrip( ',' )
-                    ldda_id_list = created_ldda_ids.split( ',' )
-                    total_added = len( ldda_id_list )
-                    if replace_dataset:
-                        msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name )
-                    else:
-                        if not folder.parent:
-                            # Libraries have the same name as their root_folder
-                            msg = "Added %d datasets to the library '%s' ( each is selected ).  " % ( total_added, folder.name )
-                        else:
-                            msg = "Added %d datasets to the folder '%s' ( each is selected ).  " % ( total_added, folder.name )
-                    # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need
-                    # to check one of them to see if the current user can manage permissions on them.
-                    check_ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id_list[0] )
-                    user, roles = trans.get_user_and_roles()
-                    if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ):
-                        if replace_dataset:
-                            default_action = ''
-                        else:
-                            msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
-                            default_action = 'manage_permissions'
-                    else:
-                        default_action = 'add'
-                    return trans.response.send_redirect( web.url_for( controller='library',
-                                                                      action='browse_library',
-                                                                      obj_id=library_id,
-                                                                      created_ldda_ids=created_ldda_ids.lstrip( ',' ),
-                                                                      default_action=default_action,
-                                                                      msg=util.sanitize_text( msg ),
-                                                                      messagetype='done' ) )
-            else:
-                msg = 'Select at least one dataset from the list of active datasets in your current history'
-                messagetype = 'error'
-                last_used_build = folder.genome_build
-                upload_option = params.get( 'upload_option', 'import_from_history' )
-                # Send list of data formats to the form so the "extension" select list can be populated dynamically
-                file_formats = trans.app.datatypes_registry.upload_file_formats
-                # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
-                def get_dbkey_options( last_used_build ):
-                    for dbkey, build_name in util.dbnames:
-                        yield build_name, dbkey, ( dbkey==last_used_build )
-                dbkeys = get_dbkey_options( last_used_build )
-                # Send list of roles to the form so the dataset can be associated with 1 or more of them.
-                roles = trans.sa_session.query( trans.app.model.Role ) \
-                                        .filter( trans.app.model.Role.table.c.deleted==False ) \
-                                        .order_by( trans.app.model.Role.table.c.name )
-                return trans.fill_template( "/library/upload.mako",
-                                            upload_option=upload_option,
-                                            library_id=library_id,
-                                            folder_id=folder_id,
-                                            replace_dataset=replace_dataset,
-                                            file_formats=file_formats,
-                                            dbkeys=dbkeys,
-                                            last_used_build=last_used_build,
-                                            roles=roles,
-                                            history=history,
-                                            widgets=[],
-                                            msg=msg,
-                                            messagetype=messagetype )
-    @web.expose
-    def datasets( self, trans, library_id, ldda_ids='', **kwd ):
-        # This method is used by the select list labeled "Perform action on selected datasets"
-        # on the analysis library browser.
-        if not ldda_ids:
-            msg = "You must select at least one dataset"
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        ldda_ids = util.listify( ldda_ids )
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        if not params.do_action:
-            msg = "You must select an action to perform on selected datasets"
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        if params.do_action == 'add':
-            history = trans.get_history()
-            for ldda_id in ldda_ids:
-                ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id )
-                hda = ldda.to_history_dataset_association( target_history=history, add_to_history = True )
-            trans.sa_session.add( history )
-            trans.sa_session.flush()
-            msg = "%i dataset(s) have been imported into your history" % len( ldda_ids )
-            return trans.response.send_redirect( web.url_for( controller='library',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='done' ) )
-        elif params.do_action == 'manage_permissions':
-            # We need the folder containing the LibraryDatasetDatasetAssociation(s)
-            ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_ids[0] )
-            trans.response.send_redirect( web.url_for( controller='library',
-                                                       action='upload_library_dataset',
-                                                       library_id=library_id,
-                                                       folder_id=ldda.library_dataset.folder.id,
-                                                       obj_id=','.join( ldda_ids ),
-                                                       permissions=True,
-                                                       msg=util.sanitize_text( msg ),
-                                                       messagetype=messagetype ) )
-        else:
-            try:
-                if params.do_action == 'zip':
-                    # Can't use mkstemp - the file must not exist first
-                    tmpd = tempfile.mkdtemp()
-                    tmpf = os.path.join( tmpd, 'library_download.' + params.do_action )
-                    if ziptype == '64':
-                        archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
-                    else:
-                        archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED )
-                    archive.add = lambda x, y: archive.write( x, y.encode('CP437') )
-                elif params.do_action == 'tgz':
-                    archive = util.streamball.StreamBall( 'w|gz' )
-                elif params.do_action == 'tbz':
-                    archive = util.streamball.StreamBall( 'w|bz2' )
-            except (OSError, zipfile.BadZipFile):
-                log.exception( "Unable to create archive for download" )
-                msg = "Unable to create archive for download, please report this error"
-                return trans.response.send_redirect( web.url_for( controller='library',
-                                                                  action='browse_library',
-                                                                  obj_id=library_id,
-                                                                  msg=util.sanitize_text( msg ),
-                                                                  messagetype='error' ) )
-            seen = []
-            user, roles = trans.get_user_and_roles()
-            for ldda_id in ldda_ids:
-                ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id )
-                if not ldda or not trans.app.security_agent.can_access_dataset( roles, ldda.dataset ):
-                    continue
-                path = ""
-                parent_folder = ldda.library_dataset.folder
-                while parent_folder is not None:
-                    # Exclude the now-hidden "root folder"
-                    if parent_folder.parent is None:
-                        path = os.path.join( parent_folder.library_root[0].name, path )
-                        break
-                    path = os.path.join( parent_folder.name, path )
-                    parent_folder = parent_folder.parent
-                path += ldda.name
-                while path in seen:
-                    path += '_'
-                seen.append( path )
-                try:
-                    archive.add( ldda.dataset.file_name, path )
-                except IOError:
-                    log.exception( "Unable to write to temporary library download archive" )
-                    msg = "Unable to create archive for download, please report this error"
-                    return trans.response.send_redirect( web.url_for( controller='library',
-                                                                      action='browse_library',
-                                                                      obj_id=library_id,
-                                                                      msg=util.sanitize_text( msg ),
-                                                                      messagetype='error' ) )
-            if params.do_action == 'zip':
-                archive.close()
-                tmpfh = open( tmpf )
-                # clean up now
-                try:
-                    os.unlink( tmpf )
-                    os.rmdir( tmpd )
-                except OSError:
-                    log.exception( "Unable to remove temporary library download archive and directory" )
-                    msg = "Unable to create archive for download, please report this error"
-                    return trans.response.send_redirect( web.url_for( controller='library',
-                                                                      action='browse_library',
-                                                                      obj_id=library_id,
-                                                                      msg=util.sanitize_text( msg ),
-                                                                      messagetype='error' ) )
-                trans.response.set_content_type( "application/x-zip-compressed" )
-                trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action
-                return tmpfh
-            else:
-                trans.response.set_content_type( "application/x-tar" )
-                trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action
-                archive.wsgi_status = trans.response.wsgi_status()
-                archive.wsgi_headeritems = trans.response.wsgi_headeritems()
-                return archive.stream
diff -r 9f966847abda -r 4743015d9a57 lib/galaxy/web/controllers/library_admin.py
--- a/lib/galaxy/web/controllers/library_admin.py	Tue Dec 22 18:49:34 2009 -0500
+++ b/lib/galaxy/web/controllers/library_admin.py	Wed Dec 23 20:26:01 2009 -0500
@@ -1,6 +1,7 @@
 import sys
 from galaxy import util
 from galaxy.web.base.controller import *
+from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.model.orm import *
 # Older py compatibility
 try:
@@ -11,199 +12,123 @@
 import logging
 log = logging.getLogger( __name__ )
+# States for passing messages
+SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
+
+class LibraryListGrid( grids.Grid ):
+    class NameColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, library ):
+            return library.name
+    class DescriptionColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, library ):
+            if library.description:
+                return library.description
+            return ''
+    class StatusColumn( grids.GridColumn ):
+        def get_value( self, trans, grid, library ):
+            if library.purged:
+                return "purged"
+            elif library.deleted:
+                return "deleted"
+            return ""
+    class DeletedColumn( grids.GridColumn ):
+       def get_accepted_filters( self ):
+           """ Returns a list of accepted filters for this column. """
+           accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" }
+           accepted_filters = []
+           for label, val in accepted_filter_labels_and_vals.items():
+               args = { self.key: val }
+               accepted_filters.append( grids.GridColumnFilter( label, args) )
+           return accepted_filters
+    # Grid definition
+    title = "Data Libraries"
+    model_class = model.Library
+    template='/admin/library/grid.mako'
+    default_sort_key = "name"
+    columns = [
+        NameColumn( "Library Name",
+                    key="name",
+                    model_class=model.Library,
+                    link=( lambda library: dict( operation="browse", id=library.id ) ),
+                    attach_popup=False,
+                    filterable="advanced" ),
+        DescriptionColumn( "Description",
+                           key="description",
+                           model_class=model.Library,
+                           attach_popup=False,
+                           filterable="advanced" ),
+        grids.GridColumn( "Created", key="create_time", format=time_ago ),
+        grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
+        StatusColumn( "Status", attach_popup=False ),
+        # Columns that are valid for filtering but are not visible.
+        DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" )
+    ]
+    columns.append( grids.MulticolFilterColumn( "Search", 
+                                                cols_to_filter=[ columns[0], columns[1] ], 
+                                                key="free-text-search",
+                                                visible=False,
+                                                filterable="standard" ) )
+    global_actions = [
+        grids.GridAction( "Create new data library", dict( controller='library_admin', action='create_library' ) )
+    ]
+    standard_filters = [
+        grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
+        grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ),
+        grids.GridColumnFilter( "Purged", args=dict( purged=True ) ),
+        grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
+    ]
+    default_filter = dict( name="All", description="All", deleted="False", purged="False" )
+    num_rows_per_page = 50
+    preserve_state = False
+    use_paging = True
+    def build_initial_query( self, session ):
+        return session.query( self.model_class )
+
 class LibraryAdmin( BaseController ):
+
+    library_list_grid = LibraryListGrid()
+
     @web.expose
     @web.require_admin
-    def browse_libraries( self, trans, **kwd ):
+    def browse_libraries( self, trans, **kwargs ):
+        if 'operation' in kwargs:
+            operation = kwargs['operation'].lower()
+            if operation == "browse":
+                return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                                  action='browse_library',
+                                                                  cntrller='library_admin',
+                                                                  **kwargs ) )
+        # Render the list view
+        return self.library_list_grid( trans, **kwargs )
+    @web.expose
+    @web.require_admin
+    def create_library( self, trans, **kwd ):
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        return trans.fill_template( '/admin/library/browse_libraries.mako', 
-                                    libraries=trans.sa_session.query( trans.app.model.Library ) \
-                                                               .filter( trans.app.model.Library.table.c.deleted==False ) \
-                                                               .order_by( trans.app.model.Library.name ),
-                                    deleted=False,
-                                    show_deleted=False,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def browse_library( self, trans, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        library_id = params.get( 'obj_id', None )
-        if not library_id:
-            # To handle bots
-            msg = "You must specify a library id."
-            return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='browse_libraries',
+        if params.get( 'new', False ):
+            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 = "" )
+            library.root_folder = root_folder
+            trans.sa_session.add_all( ( library, root_folder ) )
+            trans.sa_session.flush()
+            msg = "The new library named '%s' has been created" % library.name
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller='library_admin',
+                                                              id=trans.security.encode_id( library.id ),
                                                               msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        deleted = util.string_as_bool( params.get( 'deleted', False ) )
-        show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
-        library = trans.sa_session.query( trans.app.model.Library ).get( library_id )
-        if not library:
-            msg = "Invalid library id ( %s )." % str( library_id )
-            return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='browse_libraries',
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        created_ldda_ids = params.get( 'created_ldda_ids', '' )
-        if created_ldda_ids and not msg:
-            msg = "%d datasets are now uploading in the background to the library '%s' ( each is selected ).  " % ( len( created_ldda_ids.split( ',' ) ), library.name )
-            msg += "Do not navigate away from Galaxy or use the browser's "stop" or "reload" buttons ( on this tab ) until the upload(s) change from the "uploading" state."
-            messagetype = "info"
-        return trans.fill_template( '/admin/library/browse_library.mako', 
-                                    library=library,
-                                    deleted=deleted,
-                                    show_deleted=show_deleted,
-                                    created_ldda_ids=created_ldda_ids,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def library( self, trans, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        library_id = params.get( 'obj_id', None )
-        if params.get( 'new', False ):
-            action = 'new'
-        elif params.get( 'delete', False ):
-            action = 'delete'
-        elif params.get( 'permissions', False ):
-            action = 'permissions'
-        else:
-            action = 'information'
-        if not library_id and not action == 'new':
-            msg = "You must specify a library to %s." % action
-            return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='browse_libraries',
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        if not action == 'new':
-            library = trans.sa_session.query( trans.app.model.Library ).get( int( library_id ) )
-        if action == 'new':
-            if params.new == 'submitted':
-                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 = "" )
-                library.root_folder = root_folder
-                trans.sa_session.add_all( ( library, root_folder ) )
-                trans.sa_session.flush()
-                msg = "The new library named '%s' has been created" % library.name
-                return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                                  action='browse_library',
-                                                                  obj_id=library.id,
-                                                                  msg=util.sanitize_text( msg ),
-                                                                  messagetype='done' ) )
-            return trans.fill_template( '/admin/library/new_library.mako', msg=msg, messagetype=messagetype )
-        elif action == 'information':
-            # See if we have any associated templates
-            widgets = library.get_template_widgets( trans )
-            if params.get( 'rename_library_button', False ):
-                old_name = library.name
-                new_name = util.restore_text( params.name )
-                new_description = util.restore_text( params.description )
-                if not new_name:
-                    msg = 'Enter a valid name'
-                    return trans.fill_template( '/admin/library/library_info.mako',
-                                                library=library,
-                                                widgets=widgets,
-                                                msg=msg,
-                                                messagetype='error' )
-                else:
-                    library.name = new_name
-                    library.description = new_description
-                    # Rename the root_folder
-                    library.root_folder.name = new_name
-                    library.root_folder.description = new_description
-                    trans.sa_session.add_all( ( library, library.root_folder ) )
-                    trans.sa_session.flush()
-                    msg = "Library '%s' has been renamed to '%s'" % ( old_name, new_name )
-                    return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                                      action='library',
-                                                                      obj_id=library.id,
-                                                                      edit_info=True,
-                                                                      msg=util.sanitize_text( msg ),
-                                                                      messagetype='done' ) )
-            return trans.fill_template( '/admin/library/library_info.mako',
-                                        library=library,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif action == 'delete':
-            def delete_folder( library_folder ):
-                trans.sa_session.refresh( library_folder )
-                for folder in library_folder.folders:
-                    delete_folder( folder )
-                for library_dataset in library_folder.datasets:
-                    trans.sa_session.refresh( library_dataset )
-                    ldda = library_dataset.library_dataset_dataset_association
-                    if ldda:
-                        trans.sa_session.refresh( ldda )
-                        # We don't set ldda.dataset.deleted to True here because the cleanup_dataset script
-                        # will eventually remove it from disk.  The purge_library method below sets the dataset
-                        # to deleted.  This allows for the library to be undeleted ( before it is purged ), 
-                        # restoring all of its contents.
-                        ldda.deleted = True
-                        trans.sa_session.add( ldda )
-                    library_dataset.deleted = True
-                    trans.sa_session.add( library_dataset )
-                library_folder.deleted = True
-                trans.sa_session.add( library_folder )
-                trans.sa_session.flush()
-            trans.sa_session.refresh( library )
-            delete_folder( library.root_folder )
-            library.deleted = True
-            trans.sa_session.add( library )
-            trans.sa_session.flush()
-            msg = "Library '%s' and all of its contents have been marked deleted" % library.name
-            return trans.response.send_redirect( web.url_for( action='browse_libraries', msg=util.sanitize_text( msg ), messagetype='done' ) )
-        elif action == 'permissions':
-            if params.get( 'update_roles_button', False ):
-                # The user clicked the Save button on the 'Associate With Roles' form
-                permissions = {}
-                for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
-                    permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-                trans.app.security_agent.set_all_library_permissions( library, permissions )
-                trans.sa_session.refresh( library )
-                # Copy the permissions to the root folder
-                trans.app.security_agent.copy_library_permissions( library, library.root_folder )
-                msg = "Permissions updated for library '%s'" % library.name
-                return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                                  action='library',
-                                                                  obj_id=library.id,
-                                                                  permissions=True,
-                                                                  msg=util.sanitize_text( msg ),
-                                                                  messagetype='done' ) )
-            return trans.fill_template( '/admin/library/library_permissions.mako',
-                                        library=library,
-                                        msg=msg,
-                                        messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def deleted_libraries( self, trans, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        libraries = trans.sa_session.query( trans.app.model.Library ) \
-                                    .filter( and_( trans.app.model.Library.table.c.deleted==True,
-                                                   trans.app.model.Library.table.c.purged==False ) ) \
-                                    .order_by( trans.app.model.Library.table.c.name )
-        return trans.fill_template( '/admin/library/browse_libraries.mako', 
-                                    libraries=libraries,
-                                    deleted=True,
-                                    msg=msg,
-                                    messagetype=messagetype,
-                                    show_deleted=True )
+                                                              messagetype='done' ) )
+        return trans.fill_template( '/admin/library/new_library.mako', msg=msg, messagetype=messagetype )
     @web.expose
     @web.require_admin
     def purge_library( self, trans, **kwd ):
+        # TODO: change this function to purge_library_item, behaving similar to delete_library_item
+        # assuming we want the ability to purge libraries.
+        # This function is currently only used by the functional tests.
         params = util.Params( kwd )
-        library = trans.sa_session.query( trans.app.model.Library ).get( int( params.obj_id ) )
+        library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( params.id ) )
         def purge_folder( library_folder ):
             for lf in library_folder.folders:
                 purge_folder( lf )
@@ -232,8 +157,8 @@
             msg = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name )
             return trans.response.send_redirect( web.url_for( controller='library_admin',
                                                               action='browse_libraries',
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
+                                                              message=util.sanitize_text( msg ),
+                                                              status='error' ) )
         else:
             purge_folder( library.root_folder )
             library.purged = True
@@ -241,680 +166,9 @@
             trans.sa_session.flush()
             msg = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name
             return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='deleted_libraries',
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='done' ) )
-    @web.expose
-    @web.require_admin
-    def folder( self, trans, obj_id, library_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )            
-        if params.get( 'new', False ):
-            action = 'new'
-        elif params.get( 'delete', False ):
-            action = 'delete'
-        elif params.get( 'permissions', False ):
-            action = 'permissions'
-        else:
-            # 'information' will be the default
-            action = 'information'
-        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( obj_id ) )
-        if not folder:
-            msg = "Invalid folder specified, id: %s" % str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        if action == 'new':
-            if params.new == 'submitted':
-                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 (?)
-                new_folder.genome_build = util.dbnames.default_value
-                folder.add_folder( new_folder )
-                trans.sa_session.add( new_folder )
-                trans.sa_session.flush()
-                # New folders default to having the same permissions as their parent folder
-                trans.app.security_agent.copy_library_permissions( folder, new_folder )
-                msg = "New folder named '%s' has been added to the library" % new_folder.name
-                return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                                  action='browse_library',
-                                                                  obj_id=library_id,
-                                                                  msg=util.sanitize_text( msg ),
-                                                                  messagetype='done' ) )
-            return trans.fill_template( '/admin/library/new_folder.mako',
-                                        library_id=library_id,
-                                        folder=folder,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif action == 'information':
-            # See if we have any associated templates
-            widgets = folder.get_template_widgets( trans )
-            if params.get( 'rename_folder_button', False ):
-                old_name = folder.name
-                new_name = util.restore_text( params.name )
-                new_description = util.restore_text( params.description )
-                if not new_name:
-                    msg = 'Enter a valid name'
-                    return trans.fill_template( '/admin/library/folder_info.mako',
-                                                folder=folder,
-                                                library_id=library_id,
-                                                widgets=widgets,
-                                                msg=msg,
-                                                messagetype='error' )
-                else:
-                    folder.name = new_name
-                    folder.description = new_description
-                    trans.sa_session.add( folder )
-                    trans.sa_session.flush()
-                    msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name )
-                    return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                                      action='folder',
-                                                                      obj_id=folder.id,
-                                                                      library_id=library_id,
-                                                                      edit_info=True,
-                                                                      msg=util.sanitize_text( msg ),
-                                                                      messagetype='done' ) )
-            return trans.fill_template( '/admin/library/folder_info.mako',
-                                        folder=folder,
-                                        library_id=library_id,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif action == 'delete':
-            folder.deleted = True
-            trans.sa_session.add( folder )
-            trans.sa_session.flush()
-            msg = "Folder '%s' and all of its contents have been marked deleted" % folder.name
-            return trans.response.send_redirect( web.url_for( action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='done' ) )
-        elif action =='permissions':
-            if params.get( 'update_roles_button', False ):
-                # The user clicked the Save button on the 'Associate With Roles' form
-                permissions = {}
-                for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ]
-                    permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-                trans.app.security_agent.set_all_library_permissions( folder, permissions )
-                trans.sa_session.refresh( folder )
-                msg = "Permissions updated for folder '%s'" % folder.name
-                return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                                  action='folder',
-                                                                  obj_id=folder.id,
-                                                                  library_id=library_id,
-                                                                  permissions=True,
-                                                                  msg=util.sanitize_text( msg ),
-                                                                  messagetype='done' ) )
-            return trans.fill_template( '/admin/library/folder_permissions.mako',
-                                        folder=folder,
-                                        library_id=library_id,
-                                        msg=msg,
-                                        messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def library_dataset( self, trans, obj_id, library_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        if params.get( 'permissions', False ):
-            action = 'permissions'
-        else:
-            action = 'information'
-        library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( obj_id )
-        if not library_dataset:
-            msg = "Invalid library dataset specified, id: %s" %str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        if action == 'information':
-            if params.get( 'edit_attributes_button', False ):
-                old_name = library_dataset.name
-                new_name = util.restore_text( params.get( 'name', '' ) )
-                new_info = util.restore_text( params.get( 'info', '' ) )
-                if not new_name:
-                    msg = 'Enter a valid name'
-                    messagetype = 'error'
-                else:
-                    library_dataset.name = new_name
-                    library_dataset.info = new_info
-                    trans.sa_session.add( library_dataset )
-                    trans.sa_session.flush()
-                    msg = "Dataset '%s' has been renamed to '%s'" % ( old_name, new_name )
-                    messagetype = 'done'
-            return trans.fill_template( '/admin/library/library_dataset_info.mako',
-                                        library_dataset=library_dataset,
-                                        library_id=library_id,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif action == 'permissions':
-            if params.get( 'update_roles_button', False ):
-                # The user clicked the Save button on the 'Edit permissions and role associations' form
-                permissions = {}
-                for k, v in trans.app.model.Library.permitted_actions.items():
-                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
-                    permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-                # Set the LIBRARY permissions on the LibraryDataset
-                # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
-                trans.app.security_agent.set_all_library_permissions( library_dataset, permissions )
-                trans.sa_session.refresh( library_dataset )
-                # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
-                trans.app.security_agent.set_all_library_permissions( library_dataset.library_dataset_dataset_association, permissions )
-                trans.sa_session.refresh( library_dataset.library_dataset_dataset_association )
-                msg = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name
-            return trans.fill_template( '/admin/library/library_dataset_permissions.mako',
-                                        library_dataset=library_dataset,
-                                        library_id=library_id,
-                                        msg=msg,
-                                        messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def ldda_edit_info( self, trans, library_id, folder_id, obj_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
-        if not ldda:
-            msg = "Invalid LibraryDatasetDatasetAssociation specified, obj_id: %s" % str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        dbkey = params.get( 'dbkey', '?' )
-        if isinstance( dbkey, list ):
-            dbkey = dbkey[0]
-        file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
-        file_formats.sort()
-        # See if we have any associated templates
-        widgets = ldda.get_template_widgets( trans )
-        if params.get( 'change', False ):
-            # The user clicked the Save button on the 'Change data type' form
-            if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
-                trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
-                trans.sa_session.flush()
-                msg = "Data type changed for library dataset '%s'" % ldda.name
-                return trans.fill_template( "/admin/library/ldda_edit_info.mako", 
-                                            ldda=ldda,
-                                            library_id=library_id,
-                                            file_formats=file_formats,
-                                            widgets=widgets,
-                                            msg=msg,
-                                            messagetype=messagetype )
-            else:
-                return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % \
-                                                 ( ldda.extension, params.datatype ) )
-        elif params.get( 'save', False ):
-            # The user clicked the Save button on the 'Edit Attributes' form
-            old_name = ldda.name
-            new_name = util.restore_text( params.get( 'name', '' ) )
-            new_info = util.restore_text( params.get( 'info', '' ) )
-            new_message = util.restore_text( params.get( 'message', '' ) )
-            if not new_name:
-                msg = 'Enter a valid name'
-                messagetype = 'error'
-            else:
-                ldda.name = new_name
-                ldda.info = new_info
-                ldda.message = new_message
-                # The following for loop will save all metadata_spec items
-                for name, spec in ldda.datatype.metadata_spec.items():
-                    if spec.get("readonly"):
-                        continue
-                    optional = params.get( "is_" + name, None )
-                    if optional and optional == 'true':
-                        # optional element... == 'true' actually means it is NOT checked (and therefore ommitted)
-                        setattr( ldda.metadata, name, None )
-                    else:
-                        setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) )
-                ldda.metadata.dbkey = dbkey
-                ldda.datatype.after_setting_metadata( ldda )
-                trans.sa_session.flush()
-                msg = 'Attributes updated for library dataset %s' % ldda.name
-                messagetype = 'done'
-            return trans.fill_template( "/admin/library/ldda_edit_info.mako", 
-                                        ldda=ldda,
-                                        library_id=library_id,
-                                        file_formats=file_formats,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif params.get( 'detect', False ):
-            # The user clicked the Auto-detect button on the 'Edit Attributes' form
-            for name, spec in ldda.datatype.metadata_spec.items():
-                # We need to be careful about the attributes we are resetting
-                if name not in [ 'name', 'info', 'dbkey' ]:
-                    if spec.get( 'default' ):
-                        setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) )
-            ldda.datatype.set_meta( ldda )
-            ldda.datatype.after_setting_metadata( ldda )
-            trans.sa_session.flush()
-            msg = 'Attributes updated for library dataset %s' % ldda.name
-            return trans.fill_template( "/admin/library/ldda_edit_info.mako", 
-                                        ldda=ldda,
-                                        library_id=library_id,
-                                        file_formats=file_formats,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        elif params.get( 'delete', False ):
-            ldda.deleted = True
-            trans.sa_session.add( ldda )
-            trans.sa_session.flush()
-            msg = 'Dataset %s has been removed from this data library' % ldda.name
-            return trans.fill_template( "/admin/library/ldda_edit_info.mako", 
-                                        ldda=ldda,
-                                        library_id=library_id,
-                                        file_formats=file_formats,
-                                        widgets=widgets,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey:
-            # Copy dbkey into metadata, for backwards compatability
-            # This looks like it does nothing, but getting the dbkey
-            # returns the metadata dbkey unless it is None, in which
-            # case it resorts to the old dbkey.  Setting the dbkey
-            # sets it properly in the metadata
-            ldda.metadata.dbkey = ldda.dbkey
-        return trans.fill_template( "/admin/library/ldda_edit_info.mako", 
-                                    ldda=ldda,
-                                    library_id=library_id,
-                                    file_formats=file_formats,
-                                    widgets=widgets,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def ldda_display_info( self, trans, library_id, folder_id, obj_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
-        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
-        if not ldda:
-            msg = "Invalid LibraryDatasetDatasetAssociation specified, obj_id: %s" % str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        # See if we have any associated templates
-        widgets = ldda.get_template_widgets( trans )
-        return trans.fill_template( '/admin/library/ldda_info.mako',
-                                    ldda=ldda,
-                                    library_id=library_id,
-                                    show_deleted=show_deleted,
-                                    widgets=widgets,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def ldda_manage_permissions( self, trans, library_id, folder_id, obj_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        obj_ids = util.listify( obj_id )
-        # Display permission form, permissions will be updated for all lddas simultaneously.
-        lddas = []
-        for obj_id in [ int( obj_id ) for obj_id in obj_ids ]:
-            ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
-            if ldda is None:
-                msg = 'You specified an invalid LibraryDatasetDatasetAssociation obj_id: %s' %str( obj_id )
-                trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                           action='browse_library',
-                                                           obj_id=library_id,
-                                                           msg=util.sanitize_text( msg ),
-                                                           messagetype='error' ) )
-            lddas.append( ldda )
-        if params.get( 'update_roles_button', False ):
-            permissions = {}
-            accessible = False
-            for k, v in trans.app.model.Dataset.permitted_actions.items():
-                in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
-                # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible
-                if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
-                    if len( in_roles ) > 1:
-                        # Get the set of all users that are being associated with the dataset
-                        in_roles_set = set()
-                        for role in in_roles:
-                            in_roles_set.add( role )
-                        users_set = set()
-                        for role in in_roles:
-                            for ura in role.users:
-                                users_set.add( ura.user )
-                        # Make sure that at least 1 user has every role being associated with the dataset
-                        for user in users_set:
-                            user_roles_set = set()
-                            for ura in user.roles:
-                                user_roles_set.add( ura.role )
-                            if in_roles_set.issubset( user_roles_set ):
-                                accessible = True
-                                break
-                    else:
-                        accessible = True
-                if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
-                    # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions
-                    # TODO: keep access permissions as they originally were, rather than automatically making public
-                    permissions[ trans.app.security_agent.get_action( v.action ) ] = []
-                else:
-                    permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-            for ldda in lddas:
-                # Set the DATASET permissions on the Dataset
-                trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions )
-                trans.sa_session.refresh( ldda.dataset )
-            permissions = {}
-            for k, v in trans.app.model.Library.permitted_actions.items():
-                in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
-                permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
-            for ldda in lddas:
-                # Set the LIBRARY permissions on the LibraryDataset
-                # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
-                trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions )
-                trans.sa_session.refresh( ldda.library_dataset )
-                # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
-                trans.app.security_agent.set_all_library_permissions( ldda, permissions )
-                trans.sa_session.refresh( ldda )
-            if not accessible:
-                msg = "At least 1 user must have every role associated with accessing these %d datasets. " % len( lddas )
-                msg += "The roles you attempted to associate for access would make these datasets inaccessible by everyone, "
-                msg += "so access permissions were not set.  All other permissions were updated for the datasets."
-                messagetype = 'error'
-            else:
-                msg = "Permissions have been updated on %d datasets" % len( lddas )
-            return trans.fill_template( "/admin/library/ldda_permissions.mako",
-                                        lddas=lddas,
-                                        library_id=library_id,
-                                        msg=msg,
-                                        messagetype=messagetype )
-        if len( obj_ids ) > 1:
-            # Ensure that the permissions across all library items are identical, otherwise we can't update them together.
-            check_list = []
-            for ldda in lddas:
-                permissions = []
-                # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation
-                # will always be the same as the permissions on the associated LibraryDataset, so we only need to
-                # check one Library object
-                for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ):
-                    if library_permission.action not in permissions:
-                        permissions.append( library_permission.action )
-                for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ):
-                    if dataset_permission.action not in permissions:
-                        permissions.append( dataset_permission.action )
-                permissions.sort()
-                if not check_list:
-                    check_list = permissions
-                if permissions != check_list:
-                    msg = 'The datasets you selected do not have identical permissions, so they can not be updated together'
-                    trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                               action='browse_library',
-                                                               obj_id=library_id,
-                                                               msg=util.sanitize_text( msg ),
-                                                               messagetype='error' ) )
-        return trans.fill_template( "/admin/library/ldda_permissions.mako",
-                                    lddas=lddas,
-                                    library_id=library_id,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def upload_library_dataset( self, trans, library_id, folder_id, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        deleted = util.string_as_bool( params.get( 'deleted', False ) )
-        show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
-        dbkey = params.get( 'dbkey', '?' )
-        if isinstance( dbkey, list ):
-            last_used_build = dbkey[0]
-        else:
-            last_used_build = dbkey
-        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder_id )
-        if folder and last_used_build in [ 'None', None, '?' ]:
-            last_used_build = folder.genome_build
-        replace_id = params.get( 'replace_id', None )
-        if replace_id not in [ None, 'None' ]:
-            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( int( replace_id ) )
-            # The name is separately - by the time the new ldda is created,
-            # replace_dataset.name will point to the new ldda, not the one it's
-            # replacing.
-            replace_dataset_name = replace_dataset.name
-            if not last_used_build:
-                last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
-            # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
-            upload_option = 'upload_file'
-        else:
-            replace_dataset = None
-            upload_option = params.get( 'upload_option', 'upload_file' )
-        if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ):
-            # See if we have any inherited templates, but do not inherit contents.
-            info_association, inherited = folder.get_info_association( inherited=True )
-            if info_association:
-                template_id = str( info_association.template.id )
-                widgets = folder.get_template_widgets( trans, get_contents=False )
-            else:
-                template_id = 'None'
-                widgets = []
-            created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans,
-                                                                                           controller='library_admin',
-                                                                                           library_id=library_id,
-                                                                                           folder_id=folder_id,
-                                                                                           template_id=template_id,
-                                                                                           widgets=widgets,
-                                                                                           replace_dataset=replace_dataset,
-                                                                                           **kwd )
-            if created_outputs:
-                total_added = len( created_outputs.values() )
-                if replace_dataset:
-                    msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name )
-                else:
-                    if not folder.parent:
-                        # Libraries have the same name as their root_folder
-                        msg = "Added %d datasets to the library '%s' ( each is selected ).  " % ( total_added, folder.name )
-                    else:
-                        msg = "Added %d datasets to the folder '%s' ( each is selected ).  " % ( total_added, folder.name )
-                    msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
-                messagetype='done'
-            else:
-                msg = "Upload failed"
-                messagetype='error'
-            trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                       action='browse_library',
-                                                       obj_id=library_id,
-                                                       created_ldda_ids=",".join( [ str( v.id ) for v in created_outputs.values() ] ),
-                                                       msg=util.sanitize_text( msg ),
-                                                       messagetype=messagetype ) )
-        # See if we have any inherited templates, but do not inherit contents.
-        widgets = folder.get_template_widgets( trans, get_contents=False )
-        upload_option = params.get( 'upload_option', 'upload_file' )
-        # No dataset(s) specified, so display the upload form.  Send list of data formats to the form
-        # so the "extension" select list can be populated dynamically
-        file_formats = trans.app.datatypes_registry.upload_file_formats
-        # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
-        def get_dbkey_options( last_used_build ):
-            for dbkey, build_name in util.dbnames:
-                yield build_name, dbkey, ( dbkey==last_used_build )
-        dbkeys = get_dbkey_options( last_used_build )
-        # Send list of roles to the form so the dataset can be associated with 1 or more of them.
-        roles = trans.sa_session.query( trans.app.model.Role ) \
-                                .filter( trans.app.model.Role.table.c.deleted==False ) \
-                                .order_by( trans.app.model.Role.table.c.name )
-        # Send the current history to the form to enable importing datasets from history to library
-        history = trans.get_history()
-        trans.sa_session.refresh( history )
-        # If we're using nginx upload, override the form action
-        action = web.url_for( controller='library_admin', action='upload_library_dataset' )
-        if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
-            action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action
-        return trans.fill_template( '/admin/library/upload.mako',
-                                    upload_option=upload_option,
-                                    action=action,
-                                    library_id=library_id,
-                                    folder_id=folder_id,
-                                    replace_dataset=replace_dataset,
-                                    file_formats=file_formats,
-                                    dbkeys=dbkeys,
-                                    last_used_build=last_used_build,
-                                    roles=roles,
-                                    history=history,
-                                    widgets=widgets,
-                                    msg=msg,
-                                    messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def add_history_datasets_to_library( self, trans, library_id, folder_id, hda_ids='', **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        try:
-            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( folder_id ) )
-        except:
-            msg = "Invalid folder id: %s" % str( folder_id )
-            return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        replace_id = params.get( 'replace_id', None )
-        if replace_id:
-            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( replace_id )
-        else:
-            replace_dataset = None
-        # See if the current history is empty
-        history = trans.get_history()
-        trans.sa_session.refresh( history )
-        if not history.active_datasets:
-            msg = 'Your current history is empty'
-            return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                              action='browse_library',
-                                                              obj_id=library_id,
-                                                              msg=util.sanitize_text( msg ),
-                                                              messagetype='error' ) )
-        if params.get( 'add_history_datasets_to_library_button', False ):
-            hda_ids = util.listify( hda_ids )
-            if hda_ids:
-                dataset_names = []
-                created_ldda_ids = ''
-                for hda_id in hda_ids:
-                    hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( hda_id )
-                    if hda:
-                        ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset )
-                        created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) )
-                        dataset_names.append( ldda.name )
-                        if not replace_dataset:
-                            # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new 
-                            # LDDA and LibraryDataset.
-                            trans.app.security_agent.copy_library_permissions( folder, ldda )
-                            trans.app.security_agent.copy_library_permissions( folder, ldda.library_dataset )
-                        # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
-                        trans.app.security_agent.copy_library_permissions( ldda.library_dataset, ldda )
-                    else:
-                        msg = "The requested HistoryDatasetAssociation id %s is invalid" % str( hda_id )
-                        return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                                          action='browse_library',
-                                                                          obj_id=library_id,
-                                                                          msg=util.sanitize_text( msg ),
-                                                                          messagetype='error' ) )
-                if created_ldda_ids:
-                    created_ldda_ids = created_ldda_ids.lstrip( ',' )
-                    ldda_id_list = created_ldda_ids.split( ',' )
-                    total_added = len( ldda_id_list )
-                    if replace_dataset:
-                        msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name )
-                    else:
-                        if not folder.parent:
-                            # Libraries have the same name as their root_folder
-                            msg = "Added %d datasets to the library '%s' ( each is selected ).  " % ( total_added, folder.name )
-                        else:
-                            msg = "Added %d datasets to the folder '%s' ( each is selected ).  " % ( total_added, folder.name )
-                        msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
-                    return trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                                      action='browse_library',
-                                                                      obj_id=library_id,
-                                                                      created_ldda_ids=created_ldda_ids,
-                                                                      msg=util.sanitize_text( msg ),
-                                                                      messagetype='done' ) )
-            else:
-                msg = 'Select at least one dataset from the list of active datasets in your current history'
-                messagetype = 'error'
-                last_used_build = folder.genome_build
-                upload_option = params.get( 'upload_option', 'import_from_history' )
-                # Send list of data formats to the form so the "extension" select list can be populated dynamically
-                file_formats = trans.app.datatypes_registry.upload_file_formats
-                # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
-                def get_dbkey_options( last_used_build ):
-                    for dbkey, build_name in util.dbnames:
-                        yield build_name, dbkey, ( dbkey==last_used_build )
-                dbkeys = get_dbkey_options( last_used_build )
-                # Send list of roles to the form so the dataset can be associated with 1 or more of them.
-                roles = trans.sa_session.query( trans.app.model.Role ) \
-                                        .filter( trans.app.model.Role.table.c.deleted==False ) \
-                                        .order_by( trans.app.model.Role.table.c.name )
-                return trans.fill_template( "/admin/library/upload.mako",
-                                            upload_option=upload_option,
-                                            library_id=library_id,
-                                            folder_id=folder_id,
-                                            replace_dataset=replace_dataset,
-                                            file_formats=file_formats,
-                                            dbkeys=dbkeys,
-                                            last_used_build=last_used_build,
-                                            roles=roles,
-                                            history=history,
-                                            widgets=[],
-                                            msg=msg,
-                                            messagetype=messagetype )
-    @web.expose
-    @web.require_admin
-    def datasets( self, trans, library_id, **kwd ):
-        # This method is used by the select list labeled "Perform action on selected datasets"
-        # on the admin library browser.
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        if params.get( 'action_on_datasets_button', False ):
-            ldda_ids = util.listify( params.get( 'ldda_ids', None ) )
-            if not ldda_ids:
-                msg = "At least one dataset must be selected for %s" % params.action
-                trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                           action='browse_library',
-                                                           obj_id=library_id,
-                                                           msg=util.sanitize_text( msg ),
-                                                           messagetype='error' ) )
-            if params.action == 'manage_permissions':
-                # We need the folder containing the LibraryDatasetDatasetAssociation(s)
-                ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( int( ldda_ids[0] ) )
-                trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                           action='ldda_manage_permissions',
-                                                           library_id=library_id,
-                                                           folder_id=ldda.library_dataset.folder.id,
-                                                           obj_id=",".join( ldda_ids ),
-                                                           msg=util.sanitize_text( msg ),
-                                                           messagetype=messagetype ) )
-            elif params.action == 'delete':
-                for ldda_id in ldda_ids:
-                    ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id )
-                    ldda.deleted = True
-                    trans.sa_session.add( ldda )
-                    trans.sa_session.flush()
-                msg = "The selected datasets have been removed from this data library"
-                trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                           action='browse_library',
-                                                           obj_id=library_id,
-                                                           show_deleted=False,
-                                                           msg=util.sanitize_text( msg ),
-                                                           messagetype='done' ) )
-        else:
-            trans.response.send_redirect( web.url_for( controller='library_admin',
-                                                       action='browse_library',
-                                                       obj_id=library_id,
-                                                       msg=util.sanitize_text( msg ),
-                                                       messagetype=messagetype ) )
+                                                              action='browse_libraries',
+                                                              message=util.sanitize_text( msg ),
+                                                              status='done' ) )   
     @web.expose
     @web.require_admin
     def delete_library_item( self, trans, library_id, library_item_id, library_item_type ):
@@ -936,19 +190,21 @@
                 library_item_desc = 'Dataset'
             else:
                 library_item_desc = library_item_type.capitalize()
-            library_item = trans.sa_session.query( library_item_types[ library_item_type ] ).get( int( library_item_id ) )
+            library_item = trans.sa_session.query( library_item_types[ library_item_type ] ).get( trans.security.decode_id( library_item_id ) )
             library_item.deleted = True
             trans.sa_session.add( library_item )
             trans.sa_session.flush()
             msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( library_item_desc, library_item.name ) )
             messagetype = 'done'
         if library_item_type == 'library':
-            return self.browse_libraries( trans, msg=msg, messagetype=messagetype )
+            return self.browse_libraries( trans, message=msg, status=messagetype )
         else:
-            return self.browse_library( trans,
-                                        obj_id=library_id,
-                                        msg=msg,
-                                        messagetype=messagetype )
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller='library_admin',
+                                                              id=library_id,
+                                                              msg=msg,
+                                                              messagetype=messagetype ) )
     @web.expose
     @web.require_admin
     def undelete_library_item( self, trans, library_id, library_item_id, library_item_type ):
@@ -958,26 +214,28 @@
                                'library_dataset': trans.app.model.LibraryDataset }
         if library_item_type not in library_item_types:
             msg = 'Bad library_item_type specified: %s' % str( library_item_type )
-            messagetype = 'error'
+            status = ERROR
         else:
             if library_item_type == 'library_dataset':
                 library_item_desc = 'Dataset'
             else:
                 library_item_desc = library_item_type.capitalize()
-            library_item = trans.sa_session.query( library_item_types[ library_item_type ] ).get( int( library_item_id ) )
+            library_item = trans.sa_session.query( library_item_types[ library_item_type ] ).get( trans.security.decode_id( library_item_id ) )
             if library_item.purged:
                 msg = '%s %s has been purged, so it cannot be undeleted' % ( library_item_desc, library_item.name )
-                messagetype = 'error'
+                status = ERROR
             else:
                 library_item.deleted = False
                 trans.sa_session.add( library_item )
                 trans.sa_session.flush()
                 msg = util.sanitize_text( "%s '%s' has been marked undeleted" % ( library_item_desc, library_item.name ) )
-                messagetype = 'done'
+                status = SUCCESS
         if library_item_type == 'library':
-            return self.browse_libraries( trans, msg=msg, messagetype=messagetype )
+            return self.browse_libraries( trans, message=msg, status=status )
         else:
-            return self.browse_library( trans,
-                                        obj_id=library_id,
-                                        msg=msg,
-                                        messagetype=messagetype )
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller='library_admin',
+                                                              id=library_id,
+                                                              msg=msg,
+                                                              messagetype=status ) )
diff -r 9f966847abda -r 4743015d9a57 lib/galaxy/web/controllers/library_common.py
--- a/lib/galaxy/web/controllers/library_common.py	Tue Dec 22 18:49:34 2009 -0500
+++ b/lib/galaxy/web/controllers/library_common.py	Wed Dec 23 20:26:01 2009 -0500
@@ -7,9 +7,50 @@
 from galaxy.tools.actions import upload_common
 from galaxy.web.controllers.forms import get_all_forms
 from galaxy.model.orm import *
+from galaxy.util.streamball import StreamBall
+import logging, tempfile, zipfile, tarfile, os, sys
+
+if sys.version_info[:2] < ( 2, 6 ):
+    zipfile.BadZipFile = zipfile.error
+if sys.version_info[:2] < ( 2, 5 ):
+    zipfile.LargeZipFile = zipfile.error
log = logging.getLogger( __name__ )
+# Test for available compression types
+tmpd = tempfile.mkdtemp()
+comptypes = []
+for comptype in ( 'gz', 'bz2' ):
+    tmpf = os.path.join( tmpd, 'compression_test.tar.' + comptype )
+    try:
+        archive = tarfile.open( tmpf, 'w:' + comptype )
+        archive.close()
+        comptypes.append( comptype )
+    except tarfile.CompressionError:
+        log.exception( "Compression error when testing %s compression.  This option will be disabled for library downloads." % comptype )
+    try:
+        os.unlink( tmpf )
+    except OSError:
+        pass
+ziptype = '32'
+tmpf = os.path.join( tmpd, 'compression_test.zip' )
+try:
+    archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True )
+    archive.close()
+    comptypes.append( 'zip' )
+    ziptype = '64'
+except RuntimeError:
+    log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." )
+except (TypeError, zipfile.LargeZipFile):
+    # ZIP64 is only in Python2.5+.  Remove TypeError when 2.4 support is dropped
+    log.warning( 'Max zip file size is 2GB, ZIP64 not supported' )
+    comptypes.append( 'zip' )
+try:
+    os.unlink( tmpf )
+except OSError:
+    pass
+os.rmdir( tmpd )
+
 class LibraryCommon( BaseController ):
     @web.json
     def library_item_updates( self, trans, ids=None, states=None ):
@@ -30,11 +71,661 @@
                     force_history_refresh = False
                     rval[id] = {
                         "state": data.state,
-                        "html": unicode( trans.fill_template( "library/library_item_info.mako", ldda=data ), 'utf-8' )
+                        "html": unicode( trans.fill_template( "library/common/library_item_info.mako", ldda=data ), 'utf-8' )
                         #"force_history_refresh": force_history_refresh
                     }
         return rval
-    def upload_dataset( self, trans, controller, library_id, folder_id, replace_dataset=None, **kwd ):
+    @web.expose
+    def browse_library( self, trans, cntrller, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        library_id = params.get( 'id', None )
+        if not library_id:
+            # To handle bots
+            msg = "You must specify a library id."
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='browse_libraries',
+                                                              default_action=params.get( 'default_action', None ),
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='error' ) )
+        library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
+        if not library:
+            # To handle bots
+            msg = "Invalid library id ( %s )." % str( library_id )
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='browse_libraries',
+                                                              default_action=params.get( 'default_action', None ),
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='error' ) )
+        show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
+        created_ldda_ids = params.get( 'created_ldda_ids', '' )
+        hidden_folder_ids = util.listify( params.get( 'hidden_folder_ids', '' ) )
+        if created_ldda_ids and not msg:
+            msg = "%d datasets are now uploading in the background to the library '%s' ( each is selected ).  "  % \
+                ( len( created_ldda_ids.split( ',' ) ), library.name )
+            msg += "Do not navigate away from Galaxy or use the browser's "stop" or "reload" buttons ( on this tab ) until the upload(s) change from the "uploading" state."
+            messagetype = "info"
+        return trans.fill_template( '/library/common/browse_library.mako',
+                                    cntrller=cntrller,
+                                    library=library,
+                                    created_ldda_ids=created_ldda_ids,
+                                    hidden_folder_ids=hidden_folder_ids,
+                                    default_action=params.get( 'default_action', None ),
+                                    show_deleted=show_deleted,
+                                    comptypes=comptypes,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    def library_info( self, trans, cntrller, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        library_id = params.get( 'id', None )
+        library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
+        # See if we have any associated templates
+        widgets = library.get_template_widgets( trans )
+        if params.get( 'rename_library_button', False ):
+            old_name = library.name
+            new_name = util.restore_text( params.name )
+            new_description = util.restore_text( params.description )
+            if not new_name:
+                msg = 'Enter a valid name'
+                return trans.fill_template( '/library/common/library_info.mako',
+                                            cntrller=cntrller,
+                                            library=library,
+                                            widgets=widgets,
+                                            msg=msg,
+                                            messagetype='error' )
+            else:
+                library.name = new_name
+                library.description = new_description
+                # Rename the root_folder
+                library.root_folder.name = new_name
+                library.root_folder.description = new_description
+                trans.sa_session.add_all( ( library, library.root_folder ) )
+                trans.sa_session.flush()
+                msg = "Library '%s' has been renamed to '%s'" % ( old_name, new_name )
+                return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                                  action='library_info',
+                                                                  cntrller=cntrller,
+                                                                  id=trans.security.encode_id( library.id ),
+                                                                  msg=util.sanitize_text( msg ),
+                                                                  messagetype='done' ) )
+        return trans.fill_template( '/library/common/library_info.mako',
+                                    cntrller=cntrller,
+                                    library=library,
+                                    widgets=widgets,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    def library_permissions( self, trans, cntrller, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        library_id = params.get( 'id', None )
+        library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
+        if params.get( 'update_roles_button', False ):
+            # The user clicked the Save button on the 'Associate With Roles' form
+            permissions = {}
+            for k, v in trans.app.model.Library.permitted_actions.items():
+                in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
+                permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
+            trans.app.security_agent.set_all_library_permissions( library, permissions )
+            trans.sa_session.refresh( library )
+            # Copy the permissions to the root folder
+            trans.app.security_agent.copy_library_permissions( library, library.root_folder )
+            msg = "Permissions updated for library '%s'" % library.name
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='library_permissions',
+                                                              cntrller=cntrller,
+                                                              id=trans.security.encode_id( library.id ),
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='done' ) )
+        return trans.fill_template( '/library/common/library_permissions.mako',
+                                    cntrller=cntrller,
+                                    library=library,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    def create_folder( self, trans, cntrller, parent_id, library_id, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( parent_id ) )
+        if not folder:
+            msg = "Invalid parent folder id (%s) specified" % str( parent_id )
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller=cntrller,
+                                                              id=library_id,
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='error' ) )
+        if params.new == 'submitted':
+            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 (?)
+            new_folder.genome_build = util.dbnames.default_value
+            folder.add_folder( new_folder )
+            trans.sa_session.add( new_folder )
+            trans.sa_session.flush()
+            # New folders default to having the same permissions as their parent folder
+            trans.app.security_agent.copy_library_permissions( folder, new_folder )
+            msg = "New folder named '%s' has been added to the library" % new_folder.name
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller=cntrller,
+                                                              id=library_id,
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='done' ) )
+        return trans.fill_template( '/library/common/new_folder.mako',
+                                    cntrller=cntrller,
+                                    library_id=library_id,
+                                    folder=folder,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    def folder_info( self, trans, cntrller, id, library_id, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) )
+        if cntrller != 'library_admin':
+            user, roles = trans.get_user_and_roles()
+        # See if we have any associated templates
+        widgets = folder.get_template_widgets( trans )
+        if params.get( 'rename_folder_button', False ):
+            if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( user, roles, folder ):
+                old_name = folder.name
+                new_name = util.restore_text( params.name )
+                new_description = util.restore_text( params.description )
+                if not new_name:
+                    msg = 'Enter a valid name'
+                    return trans.fill_template( "/library/common/folder_info.mako",
+                                                cntrller=cntrller,
+                                                folder=folder,
+                                                library_id=library_id,
+                                                widgets=widgets,
+                                                msg=msg,
+                                                messagetype='error' )
+                else:
+                    folder.name = new_name
+                    folder.description = new_description
+                    trans.sa_session.add( folder )
+                    trans.sa_session.flush()
+                    msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name )
+                    return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                                      action='folder_info',
+                                                                      cntrller=cntrller,
+                                                                      id=id,
+                                                                      library_id=library_id,
+                                                                      msg=util.sanitize_text( msg ),
+                                                                      messagetype='done' ) )
+            else:
+                msg = "You are not authorized to edit this folder"
+                return trans.fill_template( "/library/common/folder_info.mako",
+                                            cntrller=cntrller,
+                                            folder=folder,
+                                            library_id=library_id,
+                                            widgets=widgets,
+                                            msg=msg,
+                                            messagetype='error' )
+        return trans.fill_template( '/library/common/folder_info.mako',
+                                    cntrller=cntrller,
+                                    folder=folder,
+                                    library_id=library_id,
+                                    widgets=widgets,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    def folder_permissions( self, trans, cntrller, id, library_id, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( id ) )
+        if not folder:
+            msg = "Invalid folder specified, id: %s" % str( id )
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller=cntrller,
+                                                              id=library_id,
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='error' ) )
+        if cntrller == 'library':
+            user, roles = trans.get_user_and_roles()
+        if params.get( 'update_roles_button', False ):
+            # The user clicked the Save button on the 'Associate With Roles' form
+            if cntrller == 'library_admin' or trans.app.security_agent.can_manage_library_item( user, roles, folder ):
+                permissions = {}
+                for k, v in trans.app.model.Library.permitted_actions.items():
+                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ]
+                    permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
+                trans.app.security_agent.set_all_library_permissions( folder, permissions )
+                trans.sa_session.refresh( folder )
+                msg = 'Permissions updated for folder %s' % folder.name
+                return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                                  action='folder_permissions',
+                                                                  id=trans.security.encode_id( folder.id ),
+                                                                  library_id=library_id,
+                                                                  msg=util.sanitize_text( msg ),
+                                                                  messagetype='done' ) )
+            else:
+                msg = "You are not authorized to manage permissions on this folder"
+                return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                                  action='folder_permissions',
+                                                                  id=trans.security.encode_id( folder.id ),
+                                                                  library_id=library_id,
+                                                                  msg=util.sanitize_text( msg ),
+                                                                  messagetype='error' ) )
+        return trans.fill_template( '/library/common/folder_permissions.mako',
+                                    cntrller=cntrller,
+                                    folder=folder,
+                                    library_id=library_id,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    def ldda_edit_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) )
+        if not ldda:
+            msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id )
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller=cntrller,
+                                                              id=library_id,
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='error' ) )
+        dbkey = params.get( 'dbkey', '?' )
+        if isinstance( dbkey, list ):
+            dbkey = dbkey[0]
+        if cntrller == 'library':
+            user, roles = trans.get_user_and_roles()
+        file_formats = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
+        file_formats.sort()
+        # See if we have any associated templates
+        widgets = ldda.get_template_widgets( trans )
+        if params.get( 'change', False ):
+            # The user clicked the Save button on the 'Change data type' form
+            if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
+                if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change:
+                    trans.app.datatypes_registry.change_datatype( ldda, params.datatype )
+                    trans.sa_session.flush()
+                    msg = "Data type changed for library dataset '%s'" % ldda.name
+                    messagetype = 'done'
+                else:
+                    msg = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype )
+                    messagetype = 'error'
+            else:
+                msg = "You are not authorized to change the data type of dataset '%s'" % ldda.name
+                messagetype = 'error'
+            return trans.fill_template( "/library/common/ldda_edit_info.mako",
+                                        cntrller=cntrller,
+                                        ldda=ldda,
+                                        library_id=library_id,
+                                        file_formats=file_formats,
+                                        widgets=widgets,
+                                        msg=msg,
+                                        messagetype=messagetype )
+        elif params.get( 'save', False ):
+            # The user clicked the Save button on the 'Edit Attributes' form
+            if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
+                old_name = ldda.name
+                new_name = util.restore_text( params.get( 'name', '' ) )
+                new_info = util.restore_text( params.get( 'info', '' ) )
+                new_message = util.restore_text( params.get( 'message', '' ) )
+                if not new_name:
+                    msg = 'Enter a valid name'
+                    messagetype = 'error'
+                else:
+                    ldda.name = new_name
+                    ldda.info = new_info
+                    ldda.message = new_message
+                    # The following for loop will save all metadata_spec items
+                    for name, spec in ldda.datatype.metadata_spec.items():
+                        if spec.get("readonly"):
+                            continue
+                        optional = params.get( "is_" + name, None )
+                        if optional and optional == 'true':
+                            # optional element... == 'true' actually means it is NOT checked (and therefore ommitted)
+                            setattr( ldda.metadata, name, None )
+                        else:
+                            setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) )
+                    ldda.metadata.dbkey = dbkey
+                    ldda.datatype.after_setting_metadata( ldda )
+                    trans.sa_session.flush()
+                    msg = 'Attributes updated for library dataset %s' % ldda.name
+                    messagetype = 'done'
+            else:
+                msg = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name
+                messagetype = 'error'
+            return trans.fill_template( "/library/common/ldda_edit_info.mako",
+                                        cntrller=cntrller,
+                                        ldda=ldda,
+                                        library_id=library_id,
+                                        file_formats=file_formats,
+                                        widgets=widgets,
+                                        msg=msg,
+                                        messagetype=messagetype )
+        elif params.get( 'detect', False ):
+            # The user clicked the Auto-detect button on the 'Edit Attributes' form
+            if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
+                for name, spec in ldda.datatype.metadata_spec.items():
+                    # We need to be careful about the attributes we are resetting
+                    if name not in [ 'name', 'info', 'dbkey' ]:
+                        if spec.get( 'default' ):
+                            setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) )
+                ldda.datatype.set_meta( ldda )
+                ldda.datatype.after_setting_metadata( ldda )
+                trans.sa_session.flush()
+                msg = 'Attributes updated for library dataset %s' % ldda.name
+                messagetype = 'done'
+            else:
+                msg = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name
+                messagetype = 'error'
+            return trans.fill_template( "/library/common/ldda_edit_info.mako",
+                                        cntrller=cntrller,
+                                        ldda=ldda,
+                                        library_id=library_id,
+                                        file_formats=file_formats,
+                                        widgets=widgets,
+                                        msg=msg,
+                                        messagetype=messagetype )
+        if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( user, roles, ldda ):
+            if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey:
+                # Copy dbkey into metadata, for backwards compatability
+                # This looks like it does nothing, but getting the dbkey
+                # returns the metadata dbkey unless it is None, in which
+                # case it resorts to the old dbkey.  Setting the dbkey
+                # sets it properly in the metadata
+                ldda.metadata.dbkey = ldda.dbkey
+        return trans.fill_template( "/library/common/ldda_edit_info.mako",
+                                    cntrller=cntrller,
+                                    ldda=ldda,
+                                    library_id=library_id,
+                                    file_formats=file_formats,
+                                    widgets=widgets,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    def ldda_display_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
+        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) )
+        if not ldda:
+            msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id )
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller=cntrller,
+                                                              id=library_id,
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='error' ) )
+        library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) )
+        # See if we have any associated templates
+        widgets = ldda.get_template_widgets( trans )
+        return trans.fill_template( '/library/common/ldda_info.mako',
+                                    cntrller=cntrller,
+                                    ldda=ldda,
+                                    library=library,
+                                    show_deleted=show_deleted,
+                                    widgets=widgets,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    def ldda_permissions( self, trans, cntrller, library_id, folder_id, id, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        ids = util.listify( id )
+        # Display permission form, permissions will be updated for all lddas simultaneously.
+        lddas = []
+        for id in [ trans.security.decode_id( id ) for id in ids ]:
+            ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( id )
+            if ldda is None:
+                msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( id )
+                trans.response.send_redirect( web.url_for( controller='library_common',
+                                                           action='browse_library',
+                                                           cntrller=cntrller,
+                                                           id=library_id,
+                                                           msg=util.sanitize_text( msg ),
+                                                           messagetype='error' ) )
+            lddas.append( ldda )
+        if params.get( 'update_roles_button', False ):
+            if cntrller=='library_admin' or ( trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \
+                                              trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ) ):
+                permissions = {}
+                accessible = False
+                for k, v in trans.app.model.Dataset.permitted_actions.items():
+                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
+                    # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible
+                    if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
+                        if len( in_roles ) > 1:
+                            # Get the set of all users that are being associated with the dataset
+                            in_roles_set = set()
+                            for role in in_roles:
+                                in_roles_set.add( role )
+                            users_set = set()
+                            for role in in_roles:
+                                for ura in role.users:
+                                    users_set.add( ura.user )
+                            # Make sure that at least 1 user has every role being associated with the dataset
+                            for user in users_set:
+                                user_roles_set = set()
+                                for ura in user.roles:
+                                    user_roles_set.add( ura.role )
+                                if in_roles_set.issubset( user_roles_set ):
+                                    accessible = True
+                                    break
+                        else:
+                            accessible = True
+                    if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
+                        # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions
+                        # TODO: keep access permissions as they originally were, rather than automatically making public
+                        permissions[ trans.app.security_agent.get_action( v.action ) ] = []
+                    else:
+                        permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
+                for ldda in lddas:
+                    # Set the DATASET permissions on the Dataset
+                    trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions )
+                    trans.sa_session.refresh( ldda.dataset )
+                permissions = {}
+                for k, v in trans.app.model.Library.permitted_actions.items():
+                    in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ]
+                    permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
+                for ldda in lddas:
+                    # Set the LIBRARY permissions on the LibraryDataset
+                    # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions
+                    trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions )
+                    trans.sa_session.refresh( ldda.library_dataset )
+                    # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation
+                    trans.app.security_agent.set_all_library_permissions( ldda, permissions )
+                    trans.sa_session.refresh( ldda )
+                if not accessible:
+                    msg = "At least 1 user must have every role associated with accessing these %d datasets. " % len( lddas )
+                    msg += "The roles you attempted to associate for access would make these datasets inaccessible by everyone, "
+                    msg += "so access permissions were not set.  All other permissions were updated for the datasets."
+                    messagetype = 'error'
+                else:
+                    msg = "Permissions have been updated on %d datasets" % len( lddas )
+            else:
+                msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name
+                messagetype = 'error'
+            return trans.fill_template( "/library/common/ldda_permissions.mako",
+                                        cntrller=cntrller,
+                                        lddas=lddas,
+                                        library_id=library_id,
+                                        msg=msg,
+                                        messagetype=messagetype )
+        if len( ids ) > 1:
+            # Ensure that the permissions across all library items are identical, otherwise we can't update them together.
+            check_list = []
+            for ldda in lddas:
+                permissions = []
+                # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation
+                # will always be the same as the permissions on the associated LibraryDataset, so we only need to
+                # check one Library object
+                for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ):
+                    if library_permission.action not in permissions:
+                        permissions.append( library_permission.action )
+                for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ):
+                    if dataset_permission.action not in permissions:
+                        permissions.append( dataset_permission.action )
+                permissions.sort()
+                if not check_list:
+                    check_list = permissions
+                if permissions != check_list:
+                    msg = 'The datasets you selected do not have identical permissions, so they can not be updated together'
+                    trans.response.send_redirect( web.url_for( controller='library_common',
+                                                               action='browse_library',
+                                                               cntrller=cntrller,
+                                                               id=library_id,
+                                                               msg=util.sanitize_text( msg ),
+                                                               messagetype='error' ) )
+        return trans.fill_template( "/library/common/ldda_permissions.mako",
+                                    cntrller=cntrller,
+                                    lddas=lddas,
+                                    library_id=library_id,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    def upload_library_dataset( self, trans, cntrller, library_id, folder_id, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        deleted = util.string_as_bool( params.get( 'deleted', False ) )
+        show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) )
+        dbkey = params.get( 'dbkey', '?' )
+        if isinstance( dbkey, list ):
+            last_used_build = dbkey[0]
+        else:
+            last_used_build = dbkey
+        folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
+        if folder and last_used_build in [ 'None', None, '?' ]:
+            last_used_build = folder.genome_build
+        replace_id = params.get( 'replace_id', None )
+        if replace_id not in [ None, 'None' ]:
+            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) )
+            # The name is separately - by the time the new ldda is created,
+            # replace_dataset.name will point to the new ldda, not the one it's
+            # replacing.
+            replace_dataset_name = replace_dataset.name
+            if not last_used_build:
+                last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
+            # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version
+            upload_option = 'upload_file'
+        else:
+            replace_dataset = None
+            upload_option = params.get( 'upload_option', 'upload_file' )
+        if cntrller == 'library':
+            user, roles = trans.get_user_and_roles()
+        if cntrller == 'library_admin' or \
+            ( trans.app.security_agent.can_add_library_item( user, roles, folder ) or \
+              ( replace_dataset and trans.app.security_agent.can_modify_library_item( user, roles, replace_dataset ) ) ):
+            if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ):
+                # See if we have any inherited templates, but do not inherit contents.
+                info_association, inherited = folder.get_info_association( inherited=True )
+                if info_association:
+                    template_id = str( info_association.template.id )
+                    widgets = folder.get_template_widgets( trans, get_contents=False )
+                else:
+                    template_id = 'None'
+                    widgets = []
+                created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans,
+                                                                                               cntrller=cntrller,
+                                                                                               library_id=library_id,
+                                                                                               folder_id=folder_id,
+                                                                                               template_id=template_id,
+                                                                                               widgets=widgets,
+                                                                                               replace_dataset=replace_dataset,
+                                                                                               **kwd )
+                if created_outputs:
+                    total_added = len( created_outputs.values() )
+                    if replace_dataset:
+                        msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name )
+                    else:
+                        if not folder.parent:
+                            # Libraries have the same name as their root_folder
+                            msg = "Added %d datasets to the library '%s' ( each is selected ).  " % ( total_added, folder.name )
+                        else:
+                            msg = "Added %d datasets to the folder '%s' ( each is selected ).  " % ( total_added, folder.name )
+                        if cntrller == 'library_admin':
+                            msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
+                            messagetype='done'
+                        else:
+                            # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need
+                            # to check one of them to see if the current user can manage permissions on them.
+                            ldda_id_list = [ str( v.id ) for v in created_outputs.values() ]
+                            check_ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id_list[0] )
+                            if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ):
+                                if replace_dataset:
+                                    default_action = ''
+                                else:
+                                    msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
+                                    default_action = 'manage_permissions'
+                            else:
+                                default_action = 'add'
+                            trans.response.send_redirect( web.url_for( controller='library_common',
+                                                                       action='browse_library',
+                                                                       cntrller=cntrller,
+                                                                       id=library_id,
+                                                                       default_action=default_action,
+                                                                       created_ldda_ids=",".join( ldda_id_list ), 
+                                                                       msg=util.sanitize_text( msg ), 
+                                                                       messagetype='done' ) )
+                    
+                else:
+                    msg = "Upload failed"
+                    messagetype='error'
+                trans.response.send_redirect( web.url_for( controller='library_common',
+                                                           action='browse_library',
+                                                           cntrller=cntrller,
+                                                           id=library_id,
+                                                           created_ldda_ids=",".join( [ str( v.id ) for v in created_outputs.values() ] ),
+                                                           msg=util.sanitize_text( msg ),
+                                                           messagetype=messagetype ) )
+        # See if we have any inherited templates, but do not inherit contents.
+        widgets = folder.get_template_widgets( trans, get_contents=False )
+        upload_option = params.get( 'upload_option', 'upload_file' )
+        # No dataset(s) specified, so display the upload form.  Send list of data formats to the form
+        # so the "extension" select list can be populated dynamically
+        file_formats = trans.app.datatypes_registry.upload_file_formats
+        # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
+        def get_dbkey_options( last_used_build ):
+            for dbkey, build_name in util.dbnames:
+                yield build_name, dbkey, ( dbkey==last_used_build )
+        dbkeys = get_dbkey_options( last_used_build )
+        # Send list of roles to the form so the dataset can be associated with 1 or more of them.
+        roles = trans.sa_session.query( trans.app.model.Role ) \
+                                .filter( trans.app.model.Role.table.c.deleted==False ) \
+                                .order_by( trans.app.model.Role.table.c.name )
+        # Send the current history to the form to enable importing datasets from history to library
+        history = trans.get_history()
+        trans.sa_session.refresh( history )
+        # If we're using nginx upload, override the form action
+        action = web.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller )
+        if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
+            action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action
+        return trans.fill_template( '/library/common/upload.mako',
+                                    cntrller=cntrller,
+                                    upload_option=upload_option,
+                                    action=action,
+                                    library_id=library_id,
+                                    folder_id=folder_id,
+                                    replace_dataset=replace_dataset,
+                                    file_formats=file_formats,
+                                    dbkeys=dbkeys,
+                                    last_used_build=last_used_build,
+                                    roles=roles,
+                                    history=history,
+                                    widgets=widgets,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd ):
         # Set up the traditional tool state/params
         tool_id = 'upload1'
         tool = trans.app.toolbox.tools_by_id[ tool_id ]
@@ -52,7 +743,7 @@
         messagetype = params.get( 'messagetype', 'done' )
         server_dir = util.restore_text( params.get( 'server_dir', '' ) )
         if replace_dataset not in [ None, 'None' ]:
-            replace_id = replace_dataset.id
+            replace_id = trans.security.encode_id( replace_dataset.id )
         else:
             replace_id = None
         upload_option = params.get( 'upload_option', 'upload_file' )
@@ -60,7 +751,7 @@
         if upload_option == 'upload_directory':
             if server_dir in [ None, 'None', '' ]:
                 err_redirect = True
-            if controller == 'library_admin':
+            if cntrller == 'library_admin':
                 import_dir = trans.app.config.library_import_dir
                 import_dir_desc = 'library_import_dir'
                 full_dir = os.path.join( import_dir, server_dir )
@@ -76,7 +767,7 @@
             else:
                 msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc
         # Proceed with (mostly) regular upload processing
-        precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=controller )
+        precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=cntrller )
         if upload_option == 'upload_file':
             tool_params = upload_common.persist_uploads( tool_params )
             uploaded_datasets = upload_common.get_uploaded_datasets( trans, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch )
@@ -89,8 +780,9 @@
             msg = 'Select a file, enter a URL or enter text'
             err_redirect = True
         if err_redirect:
-            trans.response.send_redirect( web.url_for( controller=controller,
+            trans.response.send_redirect( web.url_for( controller='library_common',
                                                        action='upload_library_dataset',
+                                                       cntrller=cntrller,
                                                        library_id=library_id,
                                                        folder_id=folder_id,
                                                        replace_id=replace_id,
@@ -182,15 +874,136 @@
             return None, err_redirect, msg
         return uploaded_datasets, None, None
     @web.expose
-    def download_dataset_from_folder( self, trans, cntrller, obj_id, library_id=None, **kwd ):
+    def add_history_datasets_to_library( self, trans, cntrller, library_id, folder_id, hda_ids='', **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        try:
+            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
+        except:
+            msg = "Invalid folder id: %s" % str( folder_id )
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller=cntrller,
+                                                              id=library_id,
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='error' ) )
+        replace_id = params.get( 'replace_id', None )
+        if replace_id:
+            replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) )
+        else:
+            replace_dataset = None
+        # See if the current history is empty
+        history = trans.get_history()
+        trans.sa_session.refresh( history )
+        if not history.active_datasets:
+            msg = 'Your current history is empty'
+            return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                              action='browse_library',
+                                                              cntrller=cntrller,
+                                                              id=library_id,
+                                                              msg=util.sanitize_text( msg ),
+                                                              messagetype='error' ) )
+        if params.get( 'add_history_datasets_to_library_button', False ):
+            hda_ids = util.listify( hda_ids )
+            if hda_ids:
+                dataset_names = []
+                created_ldda_ids = ''
+                for hda_id in hda_ids:
+                    hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id ) )
+                    if hda:
+                        ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset )
+                        created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) )
+                        dataset_names.append( ldda.name )
+                        if not replace_dataset:
+                            # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new 
+                            # LDDA and LibraryDataset.
+                            trans.app.security_agent.copy_library_permissions( folder, ldda )
+                            trans.app.security_agent.copy_library_permissions( folder, ldda.library_dataset )
+                        # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
+                        trans.app.security_agent.copy_library_permissions( ldda.library_dataset, ldda )
+                    else:
+                        msg = "The requested HistoryDatasetAssociation id %s is invalid" % str( hda_id )
+                        return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                                          action='browse_library',
+                                                                          cntrller=cntrller,
+                                                                          id=library_id,
+                                                                          msg=util.sanitize_text( msg ),
+                                                                          messagetype='error' ) )
+                if created_ldda_ids:
+                    created_ldda_ids = created_ldda_ids.lstrip( ',' )
+                    ldda_id_list = created_ldda_ids.split( ',' )
+                    total_added = len( ldda_id_list )
+                    if replace_dataset:
+                        msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name )
+                    else:
+                        if not folder.parent:
+                            # Libraries have the same name as their root_folder
+                            msg = "Added %d datasets to the library '%s' ( each is selected ).  " % ( total_added, folder.name )
+                        else:
+                            msg = "Added %d datasets to the folder '%s' ( each is selected ).  " % ( total_added, folder.name )
+                        if cntrller == 'library_admin':
+                            msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
+                        else:
+                            # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need
+                            # to check one of them to see if the current user can manage permissions on them.
+                            check_ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id_list[0] ) )
+                            user, roles = trans.get_user_and_roles()
+                            if trans.app.security_agent.can_manage_library_item( user, roles, check_ldda ):
+                                if replace_dataset:
+                                    default_action = ''
+                                else:
+                                    msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary."
+                                    default_action = 'manage_permissions'
+                            else:
+                                default_action = 'add'
+                    return trans.response.send_redirect( web.url_for( controller='library_common',
+                                                                      action='browse_library',
+                                                                      cntrller=cntrller,
+                                                                      id=library_id,
+                                                                      created_ldda_ids=created_ldda_ids,
+                                                                      msg=util.sanitize_text( msg ),
+                                                                      messagetype='done' ) )
+            else:
+                msg = 'Select at least one dataset from the list of active datasets in your current history'
+                messagetype = 'error'
+                last_used_build = folder.genome_build
+                upload_option = params.get( 'upload_option', 'import_from_history' )
+                # Send list of data formats to the form so the "extension" select list can be populated dynamically
+                file_formats = trans.app.datatypes_registry.upload_file_formats
+                # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
+                def get_dbkey_options( last_used_build ):
+                    for dbkey, build_name in util.dbnames:
+                        yield build_name, dbkey, ( dbkey==last_used_build )
+                dbkeys = get_dbkey_options( last_used_build )
+                # Send list of roles to the form so the dataset can be associated with 1 or more of them.
+                roles = trans.sa_session.query( trans.app.model.Role ) \
+                                        .filter( trans.app.model.Role.table.c.deleted==False ) \
+                                        .order_by( trans.app.model.Role.table.c.name )
+                return trans.fill_template( "/library/common/upload.mako",
+                                            upload_option=upload_option,
+                                            library_id=library_id,
+                                            folder_id=folder_id,
+                                            replace_dataset=replace_dataset,
+                                            file_formats=file_formats,
+                                            dbkeys=dbkeys,
+                                            last_used_build=last_used_build,
+                                            roles=roles,
+                                            history=history,
+                                            widgets=[],
+                                            msg=msg,
+                                            messagetype=messagetype )
+    @web.expose
+    def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **kwd ):
         """Catches the dataset id and displays file contents as directed"""
         # id must refer to a LibraryDatasetDatasetAssociation object
-        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
+        ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( id )
         if not ldda.dataset:
-            msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id )
-            return trans.response.send_redirect( web.url_for( controller=cntrller,
+            msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( id )
+            return trans.response.send_redirect( web.url_for( controller='library_common',
                                                               action='browse_library',
-                                                              obj_id=library_id,
+                                                              cntrller=cntrller,
+                                                              id=library_id,
                                                               msg=util.sanitize_text( msg ),
                                                               messagetype='error' ) )
         mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() )
@@ -200,38 +1013,263 @@
         valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
         fname = ldda.name
         fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ]
-        trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname )
+        trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( id ), fname )
         try:
             return open( ldda.file_name )
         except: 
             msg = 'This dataset contains no content'
-            return trans.response.send_redirect( web.url_for( controller=cntrller,
+            return trans.response.send_redirect( web.url_for( controller='library_common',
                                                               action='browse_library',
-                                                              obj_id=library_id,
+                                                              cntrller=cntrller,
+                                                              id=library_id,
                                                               msg=util.sanitize_text( msg ),
                                                               messagetype='error' ) )
     @web.expose
-    def info_template( self, trans, cntrller, library_id, response_action='library', obj_id=None, folder_id=None, ldda_id=None, **kwd ):

    

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[galaxy-dev] [hg] galaxy 3194: Data library cleanup