First pass of the new Galaxy forms components including requests which based on form definitions and samples.

2026-09-21 13:50:20 +08:00 · 2009-07-10 11:37:28 -04:00
parent aec2b12e5e
commit 7dafb15077
40 changed files with 3443 additions and 3 deletions
@@ -15,6 +15,7 @@ import galaxy.datatypes.registry
 from galaxy.datatypes.metadata import MetadataCollection
 from galaxy.security import RBACAgent, get_permitted_actions

+
 import logging
 log = logging.getLogger( __name__ )

@@ -1095,6 +1096,58 @@ class MetadataFile( object ):
                raise
        # Return filename inside hashed directory
        return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
+    
+    
+class FormDefinition( object ):
+    def __init__(self, name=None, desc=None, fields=[], current_form_id=None):
+        self.name = name
+        self.desc = desc
+        self.fields = fields 
+        self.form_definition_current_id = current_form_id
+        
+class FormDefinitionCurrent( object ):
+    def __init__(self, form_definition_id=None):
+        self.latest_form_id = form_definition_id
+        
+class FormValues( object ):
+    def __init__(self, form_def_id=None, content=None):
+        self.form_definition_id = form_def_id
+        self.content = content
+        
+class Request( object ):
+    def __init__(self, name=None, desc=None, request_type_id=None, user_id=None, form_values_id=None, library_id=None):
+        self.name = name
+        self.desc = desc
+        self.request_type_id = request_type_id
+        self.form_values_id = form_values_id
+        self.user_id = user_id
+        self.library_id = library_id
+        
+class RequestType( object ):
+    def __init__(self, request_form_id=None, sample_form_id=None):
+        self.request_form_id = request_form_id
+        self.sample_form_id = sample_form_id
+    
+class Sample( object ):
+    def __init__(self, name=None, desc=None, request_id=None, form_values_id=None):
+        self.name = name
+        self.desc = desc
+        self.request_id = request_id
+        self.form_values_id = form_values_id
+    
+class SampleState( object ):
+    def __init__(self, name=None, desc=None, request_type_id=None):
+        self.name = name
+        self.desc = desc
+        self.request_type_id = request_type_id
+
+class SampleEvent( object ):
+    def __init__(self, sample_id=None, sample_state_id=None, comment=''):
+        self.sample_id = sample_id
+        self.sample_state_id = sample_state_id
+        self.comment = comment
+
+

 ## ---- Utility methods -------------------------------------------------------

@@ -520,9 +520,115 @@ MetadataFile.table = Table( "metadata_file", metadata,
    Column( "deleted", Boolean, index=True, default=False ),
    Column( "purged", Boolean, index=True, default=False ) )

+
+FormDefinitionCurrent.table = Table('form_definition_current', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "latest_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+    Column( "deleted", Boolean, index=True, default=False ))
+
+# new table to store all the forms which is created by the admin
+FormDefinition.table = Table('form_definition', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "form_definition_current_id", Integer, ForeignKey( "form_definition_current.id" ), index=True ),
+    Column( "fields", JSONType()))
+
+RequestType.table = Table('request_type', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+    Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ) )
+
+FormValues.table = Table('form_values', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+    Column( "content", JSONType()) )
+
+Request.table = Table('request', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
+    Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ),
+    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
+    Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ),
+    Column( "deleted", Boolean, index=True, default=False ) )
+
+Sample.table = Table('sample', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
+    Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ),
+    Column( "deleted", Boolean, index=True, default=False ) )
+
+# new table to store all the possible sample states and the sample type it
+# belongs to
+SampleState.table = Table('sample_state', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) )
+
+SampleEvent.table = Table('sample_event', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), 
+    Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), 
+    Column( "comment", TEXT ) )
+
+
+
 # With the tables defined we can define the mappers and setup the 
 # relationships between the model objects.

+assign_mapper( context, Sample, Sample.table,
+               properties=dict( events=relation( SampleEvent, backref="sample",
+                                                 order_by=desc(SampleEvent.table.c.update_time) ),
+                              ) )
+
+assign_mapper( context, FormValues, FormValues.table, properties=None)
+
+assign_mapper( context, Request, Request.table, properties=None)
+
+assign_mapper( context, RequestType, RequestType.table,               
+               properties=dict( states=relation( SampleState, backref="request_type",
+                                                 order_by=desc(SampleState.table.c.update_time) ),
+                              ) )
+
+assign_mapper( context, FormDefinition, FormDefinition.table, properties=None)
+
+assign_mapper( context, FormDefinitionCurrent, FormDefinitionCurrent.table,
+                properties=dict( forms=relation( FormDefinition, backref='form_definition_current',
+                                                 cascade="all, delete-orphan",
+                                                 primaryjoin=( FormDefinitionCurrent.table.c.id == FormDefinition.table.c.form_definition_current_id ) ),
+                                 latest_form=relation( FormDefinition, post_update=True,
+                                                       primaryjoin=( FormDefinitionCurrent.table.c.latest_form_id == FormDefinition.table.c.id ) )
+                               ) )
+
+assign_mapper( context, SampleEvent, SampleEvent.table, properties=None)
+
+assign_mapper( context, SampleState, SampleState.table,
+               properties=None #dict( sample=relation( Sample, backref="sample" ),
+             )# )
+
 assign_mapper( context, ValidationError, ValidationError.table )

 assign_mapper( context, HistoryDatasetAssociation, HistoryDatasetAssociation.table,
@@ -590,6 +696,8 @@ assign_mapper( context, HistoryUserShareAssociation, HistoryUserShareAssociation
 assign_mapper( context, User, User.table, 
    properties=dict( histories=relation( History, backref="user",
                                         order_by=desc(History.table.c.update_time) ),
+                     requests=relation( Request, backref="user",
+                                         order_by=desc(Request.table.c.update_time) ),                    
                     active_histories=relation( History, primaryjoin=( ( History.table.c.user_id == User.table.c.id ) & ( not_( History.table.c.deleted ) ) ), order_by=desc( History.table.c.update_time ) ),
                     galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ),
                     stored_workflow_menu_entries=relation( StoredWorkflowMenuEntry, backref="user",
@@ -0,0 +1,189 @@
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from sqlalchemy.exceptions import *
+from migrate import *
+from migrate.changeset import *
+
+import datetime
+now = datetime.datetime.utcnow
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) )
+
+
+FormDefinitionCurrent_table = Table('form_definition_current', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "latest_form_id", Integer, 
+            #ForeignKey( "form_definition.id", use_alter=True, name='form_definition_current_latest_form_id_fk'), 
+            index=True ),
+    Column( "deleted", Boolean, index=True, default=False ))
+FormDefinition_table = Table('form_definition', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "form_definition_current_id", Integer, ForeignKey( "form_definition_current.id" ), index=True, nullable=False ),
+    Column( "fields", JSONType()) )
+
+FormValues_table = Table('form_values', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+    Column( "content", JSONType()) )
+
+RequestType_table = Table('request_type', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+    Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ) )
+# request table
+Request_table = Table('request', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
+    Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ),
+    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
+    Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ),
+    Column( "deleted", Boolean, index=True, default=False ) )
+
+Sample_table = Table('sample', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
+    Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ),
+    Column( "deleted", Boolean, index=True, default=False )  )
+
+SampleState_table = Table('sample_state', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "name", TrimmedString( 255 ), nullable=False ),
+    Column( "desc", TEXT ),
+    Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) )
+
+SampleEvent_table = Table('sample_event', metadata,
+    Column( "id", Integer, primary_key=True),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), 
+    Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ),
+    Column( "comment", TEXT ) )
+
+
+
+
+def upgrade():
+    # Load existing tables
+    metadata.reflect()
+    
+    # Add all of the new tables above
+#    metadata.create_all()
+    try:
+        FormDefinitionCurrent_table.create()
+    except Exception, e:
+        log.debug( "Creating form_definition_current table failed: %s" % str( e ) ) 
+    try:
+        FormDefinition_table.create()
+    except Exception, e:
+        log.debug( "Creating form_definition table failed: %s" % str( e ) )
+    # Add 1 foreign key constraint to the form_definition_current table
+    if FormDefinitionCurrent_table and FormDefinition_table:
+        try:
+            cons = ForeignKeyConstraint( [FormDefinitionCurrent_table.c.latest_form_id],
+                                         [FormDefinition_table.c.id],
+                                         name='form_definition_current_latest_form_id_fk' )
+            # Create the constraint
+            cons.create()
+        except Exception, e:
+            log.debug( "Adding foreign key constraint 'form_definition_current_latest_form_id_fk' to table 'form_definition_current' failed: %s" % ( str( e ) ) )
+    try:
+        FormValues_table.create()
+    except Exception, e:
+        log.debug( "Creating form_values table failed: %s" % str( e ) )  
+    try:
+        RequestType_table.create()
+    except Exception, e:
+        log.debug( "Creating request_type table failed: %s" % str( e ) )  
+    try:
+        Request_table.create()
+    except Exception, e:
+        log.debug( "Creating request table failed: %s" % str( e ) )  
+    try:
+        Sample_table.create()
+    except Exception, e:
+        log.debug( "Creating sample table failed: %s" % str( e ) )  
+    try:
+        SampleState_table.create()
+    except Exception, e:
+        log.debug( "Creating sample_state table failed: %s" % str( e ) )  
+    try:
+        SampleEvent_table.create()
+    except Exception, e:
+        log.debug( "Creating sample_event table failed: %s" % str( e ) )  
+    
+ 
+
+def downgrade():
+    # Load existing tables
+    metadata.reflect()
+    try:
+        FormDefinition_table.drop()
+    except Exception, e:
+        log.debug( "Dropping form_definition table failed: %s" % str( e ) )  
+    try:
+        FormDefinitionCurrent_table.drop()
+    except Exception, e:
+        log.debug( "Dropping form_definition_current table failed: %s" % str( e ) )  
+    try:
+        FormValues_table.drop()
+    except Exception, e:
+        log.debug( "Dropping form_values table failed: %s" % str( e ) )  
+    try:
+        Request_table.drop()
+    except Exception, e:
+        log.debug( "Dropping request table failed: %s" % str( e ) )  
+    try:
+        RequestType_table.drop()
+    except Exception, e:
+        log.debug( "Dropping request_type table failed: %s" % str( e ) )  
+    try:
+        Sample_table.drop()
+    except Exception, e:
+        log.debug( "Dropping sample table failed: %s" % str( e ) )  
+    try:
+        SampleState_table.drop()
+    except Exception, e:
+        log.debug( "Dropping sample_state table failed: %s" % str( e ) )  
+    try:
+        SampleEvent_table.drop()
+    except Exception, e:
+        log.debug( "Dropping sample_event table failed: %s" % str( e ) )      
+        
+        
+        
+          
@@ -3,6 +3,7 @@ from datetime import datetime, timedelta
 from galaxy import util, datatypes
 from galaxy.web.base.controller import *
 from galaxy.model.orm import *
+import sys

 import logging
 log = logging.getLogger( __name__ )
@@ -2097,4 +2098,123 @@ class Admin( BaseController ):
            else:
                last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 )
        return trans.fill_template( '/admin/jobs.mako', jobs = jobs, last_updated = last_updated, cutoff = cutoff, msg = msg, messagetype = messagetype )
-
+   
+    def _get_all_forms(self, trans, all_versions=False):
+        '''
+        This method returns all the latest forms from the 
+        form_definition_current table if all_versions is set to True. Otherwise
+        this method return all the versions of all the forms from form_definition
+        table
+        '''
+        if all_versions:
+            return trans.app.model.FormDefinition.query().all()
+        else:
+            fdc_list = trans.app.model.FormDefinitionCurrent.query().all()
+            return [fdc.latest_form for fdc in fdc_list]
+    @web.expose
+    @web.require_admin
+    def manage_request_types( self, trans, **kwd ):       
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        forms = self._get_all_forms(trans, all_versions=True)
+        return trans.fill_template( '/admin/requests/manage_request_types.mako', 
+                                    request_types=trans.app.model.RequestType.query().all(),
+                                    forms=forms,
+                                    deleted=False,
+                                    show_deleted=False,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    @web.require_admin
+    def request_type( self, trans, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )   
+        if params.get('create', False) == 'True':
+            return trans.fill_template( '/admin/requests/create_request_type.mako', 
+                                        forms=self._get_all_forms(trans, all_versions=False),
+                                        msg=msg,
+                                        messagetype=messagetype)
+        elif params.get('add_states', False) == 'True':
+            return trans.fill_template( '/admin/requests/add_states.mako',
+                                        sample_type_name=util.restore_text( params.name ),
+                                        desc=util.restore_text( params.description ),
+                                        num_states=int(util.restore_text( params.num_states )),
+                                        request_form_id=int(util.restore_text( params.request_form_id )),
+                                        sample_form_id=int(util.restore_text( params.sample_form_id )),
+                                        msg=msg,
+                                        messagetype=messagetype)            
+        elif params.get('save_new', False) == 'True':
+            st, msg = self._save_request_type(trans, params, None)
+            if not st:
+                return trans.fill_template( '/admin/requests/create_request_type.mako', 
+                                            forms=self._get_all_forms(trans, all_versions=False),
+                                            msg=msg,
+                                            messagetype='error')
+            return trans.fill_template( '/admin/requests/manage_request_types.mako', 
+                                        request_types=trans.app.model.RequestType.query().all(),
+                                        forms=self._get_all_forms(trans, all_versions=True),
+                                        deleted=False,
+                                        show_deleted=False,
+                                        msg=msg,
+                                        messagetype=messagetype )
+        elif params.get('edit', False) == 'True':
+            rt = trans.app.model.RequestType.get(int(util.restore_text( params.id )))
+            ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all()
+            return trans.fill_template( '/admin/requests/edit_request_type.mako', 
+                                        request_type=rt,
+                                        forms=self._get_all_forms(trans, all_versions=False),
+                                        states_list=ss_list,
+                                        deleted=False,
+                                        show_deleted=False,
+                                        msg=msg,
+                                        messagetype=messagetype )
+        elif params.get('save_changes', False) == 'True':
+            st = trans.app.model.SampleType.get(int(util.restore_text( params.id )))
+            st, msg = self._save_sample_type(trans, params, st.id)
+            if st:
+                msg = "The sample type '%s' has been updated with the changes." % st.name
+                messagetype = 'done'
+            else:
+                messagetype = 'error'
+            ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.sample_type_id == st.id).all()
+            return trans.fill_template( '/admin/samples/edit_sample_type.mako', 
+                                        sample_type=st,
+                                        forms=self._get_all_forms(trans, all_versions=False),
+                                        states_list=ss_list,
+                                        deleted=False,
+                                        show_deleted=False,
+                                        msg=msg,
+                                        messagetype=messagetype )
+    def _save_request_type(self, trans, params, request_type_id):
+        num_states = int( params.get( 'num_states', 0 ) )
+        proceed = True
+        for i in range( num_states ):
+            if not params.get( 'new_element_name_%i' % i, None ):
+                proceed = False
+                break
+        if not proceed:
+            msg = "All the state name(s) must be completed."
+            return None, msg
+        if not request_type_id: # create a new sample type to save
+            rt = trans.app.model.RequestType() 
+        else:           # use the existing sample type to save changes
+            rt = trans.app.model.RequestType.get(request_type_id)
+        rt.name = util.restore_text( params.name ) 
+        rt.desc = util.restore_text( params.description ) or ""
+        rt.request_form_id = int(util.restore_text( params.request_form_id ))
+        rt.sample_form_id = int(util.restore_text( params.sample_form_id ))
+        rt.flush()
+        # set sample states
+        ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all()
+        for ss in ss_list:
+            ss.delete()
+            ss.flush()
+        for i in range( num_states ):
+            name = params.get( 'new_element_name_%i' % i, None )
+            desc = params.get( 'new_element_description_%i' % i, None )
+            ss = trans.app.model.SampleState(name, desc, rt.id) 
+            ss.flush()
+        msg = "The new sample type named '%s' with %s state(s) has been created" % (rt.name, num_states)
+        return rt, msg
@@ -0,0 +1,323 @@
+from galaxy.web.base.controller import *
+from galaxy.model.orm import *
+from galaxy.datatypes import sniff
+from galaxy import util
+import logging, os, sys
+from galaxy.web.form_builder import * 
+from galaxy.tools.parameters.basic import parameter_types 
+from elementtree.ElementTree import XML, Element
+from galaxy.util.odict import odict
+import copy
+
+log = logging.getLogger( __name__ )
+
+
+class Forms( BaseController ):
+    @web.expose
+    @web.require_admin
+    def index( self, trans, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        return trans.fill_template( "/sample/index.mako",
+                                    default_action=params.get( 'default_action', None ),
+                                    msg=msg,
+                                    messagetype=messagetype )
+    @web.expose
+    @web.require_admin
+    def manage( self, trans, **kwd ):       
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        return self._show_forms_list(trans, msg, messagetype)
+    def _show_forms_list(self, trans, msg, messagetype):
+        fdc_list = trans.app.model.FormDefinitionCurrent.query().all()
+        return trans.fill_template( '/admin/forms/manage_forms.mako', 
+                                    fdc_list=fdc_list,
+                                    deleted=False,
+                                    show_deleted=False,
+                                    msg=msg,
+                                    messagetype=messagetype )
+    def _get_all_forms(self, trans, all_versions=False):
+        '''
+        This method returns all the latest forms from the 
+        form_definition_current table if all_versions is set to True. Otherwise
+        this method return all the versions of all the forms from form_definition
+        table
+        '''
+        if all_versions:
+            return trans.app.model.FormDefinition.query().all()
+        else:
+            fdc_list = trans.app.model.FormDefinitionCurrent.query().all()
+            return [fdc.latest_form for fdc in fdc_list]
+    @web.expose
+    @web.require_admin
+    def new( self, trans, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )   
+        if params.get('new', False) and not params.get('create_form', False):
+            self.current_form = {}
+            self.current_form['name'] = 'New Form'
+            self.current_form['desc'] = ''
+            self.current_form['fields'] = []
+            inputs = [ ( 'Name', TextField('name', 40,self.current_form['name'] ) ),
+                       ( 'Description', TextField('description', 40, self.current_form['desc']) ) ]
+            return trans.fill_template( '/admin/forms/create_form.mako', 
+                                        inputs=inputs,
+                                        msg=msg,
+                                        messagetype=messagetype )     
+        elif params.get('create_form', False) == 'True':   
+            if 'submitted' in params.new:
+                self.num_add_fields = 0
+                fd, msg = self.__save_form(trans, params)
+                self.__get_saved_form(fd)
+                return self._show_forms_list(trans, msg, messagetype)
+    @web.expose
+    @web.require_admin
+    def edit( self, trans, **kwd ):
+        '''
+        This callback method is for handling all the editing functions like:
+        remaning fields, adding/deleting fields, changing fields attributes 
+        '''
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        fd = trans.app.model.FormDefinition.get(int(util.restore_text( params.form_id )))
+        # SHOW THE FORM FOR EDITING.
+        if params.get('show_form', False) == 'True':
+            self.__get_saved_form(fd)
+            # the following two dicts store the unsaved select box options
+            self.del_options = {}
+            self.add_options = {}
+            return self.__show(trans, params, fd)
+        # DELETE FIELD
+        elif params.get('remove_button', False):
+            self.__update_current_form(params)
+            index = int(params.get('remove_button', None).split(' ')[2])-1
+            self.__remove_field(index)
+            return self.__show(trans, params, fd)            
+        # SAVE CHANGES
+        elif params.get('save_changes_button', False) == 'Save':
+            self.__update_current_form(params)
+            fd_new, msg = self.__save_form(trans, params, fd.form_definition_current.id)
+            if not fd_new:
+                return self.__show(trans, params, fd, msg, 'error')
+            else:
+                fd = fd_new
+            msg = "The form '%s' has been updated with the changes." % fd.name
+            return self.__show(trans, params, fd, msg)
+        #ADD A FIELD
+        elif params.get('add_field_button', False) == 'Add field':
+            self.__update_current_form(params)
+            self.__add_field()
+            # show the form again with one empty field
+            return self.__show(trans, params, fd)
+        # SHOW FORM READ ONLY
+        elif params.get('read_only', False):           
+            return trans.fill_template( '/admin/forms/show_form_read_only.mako',
+                                        form=fd,
+                                        msg=msg,
+                                        messagetype=messagetype )
+        # REFRESH PAGE, SelectField is selected/deselected as the type of a field
+        elif params.get('refresh', False) == 'true':
+            self.__update_current_form(params)
+            return self.__show(trans, params, fd)
+        # REMOVE SelectField OPTION
+        elif params.get('select_box_options', False) == 'remove':
+            #self.__update_current_form(params)
+            index = int(params.get( 'field_index', None ))
+            option = int(params.get( 'option_index', None ))
+            del self.current_form['fields'][index]['selectlist'][option]
+            return self.__show(trans, params, fd)
+        # ADD SelectField OPTION
+        elif params.get('select_box_options', False) == 'add':
+            #self.__update_current_form(params)
+            index = int(params.get( 'field_index', None ))
+            self.current_form['fields'][index]['selectlist'].append('')
+            return self.__show(trans, params, fd)           
+    def __remove_field(self, index):
+        del self.current_form['fields'][index]
+    def __add_field(self):
+        '''
+        add an empty field to the fields list
+        '''
+        empty_field = { 'label': '', 
+                        'helptext': '', 
+                        'visible': True,
+                        'required': False,
+                        'type': BaseField.form_field_types()[0],
+                        'selectlist': '' }
+        self.current_form['fields'].append(empty_field)
+    def __get_field(self, params, index):
+        name = params.get( 'field_name_%i' % index, None )
+        helptext = params.get( 'field_helptext_%i' % index, None )
+        required = params.get( 'field_required_%i' % index, False )
+        field_type = params.get( 'field_type_%i' % index, None )
+        if field_type == 'SelectField':
+            selectlist = self.__get_selectbox_options(params, index)
+        else:
+            selectlist = None
+        return {'label': name, 
+                'helptext': helptext, 
+                'visible': True,
+                'required': required,
+                'type': field_type,
+                'selectlist': selectlist }
+    def __get_selectbox_options(self, params, index):
+        '''
+        This method gets all the options entered by the user for field when
+        the fieldtype is SelectField 
+        '''
+        ctr=0
+        sb_options = []
+        while True:
+            option = params.get( 'field_'+str(index)+'_option_'+str(ctr), None )
+            ctr = ctr+1
+            if option:
+                sb_options.append(option)
+            else:
+                return sb_options
+    def __get_saved_form(self, fd):
+        self.current_form = {}
+        self.current_form['name'] = fd.name
+        self.current_form['desc'] = fd.desc
+        self.current_form['fields'] = list(copy.deepcopy(fd.fields))
+    def __validate_form(self, params):
+        '''
+        This method checks the following text inputs are filled out by the user
+        - the name of form
+        - name of all the fields
+        '''
+        # form name
+        if not util.restore_text( params.name ):
+            return None, 'Form name must be filled.'
+        # fields
+        for i in range( len(self.current_form['fields']) ):
+            if not params.get( 'field_name_%i' % i, None ):
+                return None, "All the field label(s) must be completed."
+        return True, ''
+    def __get_form(self, params):
+        name = util.restore_text( params.name ) 
+        desc = util.restore_text( params.description ) or ""
+        # set form fields
+        fields = []
+        for i in range( len(self.current_form['fields']) ):
+            fields.append(self.__get_field(params, i))
+        fields = fields
+        return name, desc, fields
+    def __update_current_form(self, params):
+        name, desc, fields = self.__get_form(params)
+        self.current_form = {}
+        self.current_form['name'] = name
+        self.current_form['desc'] = desc
+        self.current_form['fields'] = fields
+        
+    def __save_form(self, trans, params, fdc_id=None):
+        '''
+        This method saves the current form 
+        '''
+        # check the form for invalid inputs
+        flag, msg = self.__validate_form(params)
+        if not flag:
+            return None, msg
+        fd = trans.app.model.FormDefinition()
+        fd.name, fd.desc, fd.fields = self.__get_form(params)
+        if fdc_id: # save changes to the existing form    
+            # change the pointer in the form_definition_current table to point 
+            # to this new record
+            fdc = trans.app.model.FormDefinitionCurrent.get(fdc_id)
+        else: # create a new form
+            fdc = trans.app.model.FormDefinitionCurrent()
+        # create corresponding row in the form_definition_current table
+        fd.form_definition_current = fdc
+        fdc.latest_form = fd
+        trans.sa_session.save_or_update( fdc )
+        trans.sa_session.flush()
+        msg = "The new form named '%s' has been created. " % (fd.name)
+        request_types = trans.app.model.RequestType.query().all()
+        if not request_types:
+            msg = msg + "Now you can create requests to associate with this form."
+        return fd, msg
+    
+    class FieldUI(object):
+        def __init__(self, index, field=None, field_type=None):
+            '''
+            This method returns a list of widgets which describes a field. This 
+            includes label, helptext, type, & required/optional
+            '''
+            self.index = index
+            self.label = TextField('field_name_'+str(index), 40, '')
+            self.helptext = TextField('field_helptext_'+str(index), 40, '')
+            self.fieldtype = SelectField('field_type_'+str(index), 
+                                         refresh_on_change=True, 
+                                         refresh_on_change_values=['SelectField'])
+            self.selectbox_options = []
+            for ft in BaseField.form_field_types():
+                self.fieldtype.add_option(ft, ft)
+            self.required = SelectField('field_required_'+str(index), display='radio')
+            self.required.add_option('Required', 'true')
+            self.required.add_option('Optional', 'true', selected=True)
+            if field:
+                self.fill(field, field_type)
+        def fill(self, field, field_type=None):
+            # label
+            self.label.value = field['label']
+            # helptext
+            self.helptext.value = field['helptext']
+            # type
+            self.fieldtype = SelectField('field_type_'+str(self.index), 
+                                         refresh_on_change=True, 
+                                         refresh_on_change_values=['SelectField'])
+            if field_type:
+                field['type'] = unicode(field_type)
+            if field_type == 'SelectField' and not field['selectlist']:
+                field['selectlist'] = ['', '']
+            for ft in BaseField.form_field_types():
+                if ft == field['type']:
+                    self.fieldtype.add_option(ft, ft, selected=True)
+                    if ft == 'SelectField':
+                        self.selectbox_ui(field)
+                else:
+                    self.fieldtype.add_option(ft, ft)
+            # required/optional
+            if field['required']:
+                self.required = SelectField('required_'+str(self.index), display='radio')
+                self.required.add_option('Required', 'true', selected=True)
+                self.required.add_option('Optional', 'true')
+        def selectbox_ui(self, field):
+            self.selectbox_options = []
+            if field['selectlist']:
+                for ctr, option in enumerate(field['selectlist']):
+                    self.selectbox_options.append(('Option '+str(ctr+1),
+                                                   TextField('field_'+str(self.index)+'_option_'+str(ctr), 
+                                                            40, option)))
+        def get(self):
+            return [( 'Label', self.label ),
+                    ( 'Help text', self.helptext ),
+                    ( 'Type', self.fieldtype, self.selectbox_options),
+                    ( '', self.required)]
+        def __repr__(self):
+            return str(self.index)+'.'+self.label 
+        def label(self):
+            return str(self.index)+'.'+self.label 
+        
+    def __show(self, trans, params, form, msg=None, messagetype='done'):
+        '''
+        This method displays the form and any of the changes made to it
+        '''
+        # name & description
+        form_details = [ ( 'Name', TextField('name', 40, self.current_form['name']) ),
+                         ( 'Description', TextField('description', 40, self.current_form['desc']) ) ]
+        # fields
+        field_details = []
+        for index, field in enumerate(self.current_form['fields']):
+            field_ui = self.FieldUI(index, field)
+            field_details.append( field_ui.get() )
+        return trans.fill_template( '/admin/forms/edit_form.mako',
+                                    form_details=form_details,
+                                    field_details=field_details,
+                                    form=form,
+                                    field_types=BaseField.form_field_types(),
+                                    msg=msg,
+                                    messagetype=messagetype )
@@ -0,0 +1,429 @@
+from galaxy.web.base.controller import *
+from galaxy.web.framework.helpers import time_ago, iff, grids
+from galaxy.model.orm import *
+from galaxy.datatypes import sniff
+from galaxy import util
+from galaxy.util.streamball import StreamBall
+import logging, tempfile, zipfile, tarfile, os, sys
+from galaxy.web.form_builder import * 
+
+log = logging.getLogger( __name__ )
+
+# States for passing messages
+SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
+
+class RequestsListGrid( grids.Grid ):
+    title = "Requests"
+    model_class = model.Request
+    default_sort_key = "-create_time"
+    columns = [
+        grids.GridColumn( "Name", key="name",
+                          link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ),
+                          attach_popup=True ),
+        grids.GridColumn( "Description", key='desc'),
+        grids.GridColumn( "Sample(s)", method='number_of_samples', 
+                          link=( lambda item: iff( item.deleted, None, dict( operation="samples", id=item.id ) ) ), ),
+        grids.GridColumn( "Type", key="request_type_id", method='get_request_type'),
+        grids.GridColumn( "Last update", key="update_time", format=time_ago )
+    ]
+    operations = [
+#        grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted )  ),
+        grids.GridOperation( "Samples", allow_multiple=False, condition=( lambda item: not item.deleted )  ),
+#        grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
+#        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),
+    ]
+    standard_filters = [
+        grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
+        grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
+        grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
+    ]
+    #default_filter = dict( deleted=False )
+    def get_current_item( self, trans ):
+        return None
+    def get_request_type(self, trans, request):
+        request_type = trans.app.model.RequestType.get(request.request_type_id)
+        return request_type.name
+    def apply_default_filter( self, trans, query ):
+        return query.filter_by( user=trans.user )
+    def number_of_samples(self, trans, request):
+        return str(len(trans.app.model.Sample.filter(trans.app.model.Sample.table.c.request_id==request.id).all()))
+    
+class SamplesListGrid( grids.Grid ):
+    model_class = model.Sample
+    default_sort_key = "-create_time"
+    columns = [
+        grids.GridColumn( "Name", key="name",
+                          link=( lambda item: iff( item.deleted, None, dict( operation="show_sample", id=item.id ) ) ),
+                          attach_popup=True ),
+        grids.GridColumn( "Description", key='desc' ),
+        grids.GridColumn( "Status", method="get_status",
+                          link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) )),
+
+        grids.GridColumn( "Last update", key="update_time", format=time_ago )
+        
+        # Valid for filtering but invisible
+        #grids.GridColumn( "Deleted", key="deleted", visible=False )
+    ]
+    operations = [
+#        grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted )  ),
+#        grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
+#        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),
+        
+    ]
+    standard_filters = [
+        grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
+        grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
+        grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
+    ]
+    def __init__(self, request):
+        self.request  = request
+    def get_current_item( self, trans ):
+        return None
+    def apply_default_filter( self, trans, query ):
+        return query.filter_by( request_id=self.request.id )
+    def get_status(self, trans, sample):
+        all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all()
+        curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+        return curr_state.name
+
+class Requests( BaseController ):
+    request_grid = RequestsListGrid()
+
+    @web.expose
+    def index( self, trans ):
+        return trans.fill_template( "requests/index.mako" )
+    def get_authorized_libs(self, trans):
+        all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all()
+        authorized_libraries = []
+        for library in all_libraries:
+            if trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library) or trans.app.security_agent.check_folder_contents(trans.user, library) or trans.app.security_agent.show_library_item(trans.user, library):
+                authorized_libraries.append(library)
+        return authorized_libraries
+    @web.expose
+    def list( self, trans, **kwargs ):
+        '''
+        List all request made by the current user
+        '''
+        status = message = None
+        if 'operation' in kwargs:
+            operation = kwargs['operation'].lower()
+            if operation == "show_request":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.show_read_only(trans, id)
+            elif operation == "samples":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.show_samples(trans, id, kwargs)
+            elif operation == "show_sample":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.show_sample_read_only(trans, id)
+            elif operation == "events":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.show_events(trans, id)
+        # Render the list view
+        return self.request_grid( trans, status=status, message=message, template='/requests/grid.mako', **kwargs )
+    def show_samples(self, trans, id, kwargs):
+        '''
+        Shows all the samples associated with this request
+        '''
+        status = message = None
+        request = trans.app.model.Request.get(id)
+        self.samples_grid = SamplesListGrid(request)
+        return self.samples_grid( trans, status=status, message=message, template='/sample/grid.mako', **kwargs )        
+    def show_read_only(self, trans, id):
+        '''
+        Shows the request details
+        '''
+        request = trans.app.model.Request.get(id)
+        request_type = trans.app.model.RequestType.get(request.request_type_id)
+        request_form = trans.app.model.FormDefinition.get(request_type.request_form_id)
+        request_values = trans.app.model.FormValues.get(request.form_values_id)
+        libraries = self.get_authorized_libs(trans)
+        # list of widgets to be rendered on the request form
+        request_details = []
+        # main details
+        request_details.append(dict(label='Name', 
+                                    value=request.name, 
+                                    helptext=''))
+        request_details.append(dict(label='Description', 
+                                    value=request.desc, 
+                                    helptext=''))
+        request_details.append(dict(label='Type', 
+                                    value=request_type.name, 
+                                    helptext=''))
+        request_details.append(dict(label='Date created', 
+                                    value=request.create_time, 
+                                    helptext=''))
+        request_details.append(dict(label='Date updated', 
+                                    value=request.create_time, 
+                                    helptext=''))
+        request_details.append(dict(label='User', 
+                                    value=str(trans.user.email), 
+                                    helptext=''))
+        # library associated
+        request_details.append(dict(label='Library', 
+                                    value=trans.app.model.Library.get(request.library_id).name, 
+                                    helptext='Associated library where the resultant \
+                                              dataset will be stored'))
+        # form fields
+        for field in request_form.fields:
+            if field['required']:
+                req = 'Required'
+            else:
+                req = 'Optional'
+            request_details.append(dict(label=field['label'],
+                                        value=request_values.content[field['label']],
+                                        helptext=field['helptext']+' ('+req+')'))
+        return trans.fill_template( '/requests/view_request.mako',
+                                    request_form_id=request_form.id, 
+                                    request_details=request_details,
+                                    request_type=request_type)    
+    @web.expose
+    def new(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        if params.get('select_request_type', False) == 'True':
+            return trans.fill_template( '/requests/select_request_type.mako', 
+                                        request_types=trans.app.model.RequestType.query().all(),
+                                        libraries=self.get_authorized_libs(trans),
+                                        msg=msg,
+                                        messagetype=messagetype )
+        elif params.get('create', False) == 'True':
+            request_type_id = int(util.restore_text( params.request_type_id ))
+            return self.__show_request_form(trans, params, request_type_id)
+        elif params.get('save', False) == 'True':
+            request = self.__save(trans, params)
+            msg = 'The new request named %s has been created' % request.name
+            request_type_id = int(util.restore_text( params.request_type_id ))
+            return trans.response.send_redirect( web.url_for( controller='requests',
+                                                              action='list',
+                                                              msg=msg ,
+                                                              messagetype='done') )
+            return self.__show_request_form(trans, params, request_type_id, request=request)
+    def __save(self, trans, params, request_id=None):
+        '''
+        This method save a new request if request_id is None. 
+        '''
+        if not request_id:
+            request_type_id = int(util.restore_text( params.request_type_id ))
+            request_form_id = trans.app.model.RequestType.get(request_type_id).request_form_id
+            request_form = trans.app.model.FormDefinition.get(request_form_id)
+        else:
+            request = trans.app.model.Request.get(request_id)
+            form_values = trans.app.model.FormValues.get(request.form_values_id)
+            request_form = trans.app.model.FormDefinition.get(form_values.request_form_id)
+        name = params.get('name', '')
+        desc = params.get('desc', '')
+        library_id = params.get('library', '')
+        values = {}
+        for field in request_form.fields:
+            values[field['label']] = params.get(field['label'], '')
+        if not request_id:
+            form_values = trans.app.model.FormValues(request_form_id, values)
+            form_values.flush()
+            request = trans.app.model.Request(name, desc, request_type_id, 
+                                              trans.user.id, form_values.id,
+                                              library_id)
+            request.flush()
+        else:
+            form_values.content = values
+            form_values.flush()
+        return request
+    def __show_request_form(self, trans, params, request_type_id, request=None):
+        request_type = trans.app.model.RequestType.get(request_type_id)
+        request_form_id = request_type.request_form_id
+        if request:
+            form_values = trans.app.model.FormValues.get(request.form_values_id)
+        else:
+            form_values = None
+        # list of widgets to be rendered on the request form
+        widgets = []
+        widgets.append(dict(label='Name', 
+                            widget=TextField('name'), 
+                            helptext='(Required)'))
+        widgets.append(dict(label='Description', 
+                            widget=TextField('desc'), 
+                            helptext='(Optional)'))
+        widgets[0]['widget'].set_size(40)
+        widgets[1]['widget'].set_size(40)
+        # libraries selectbox
+        libraries = self.get_authorized_libs(trans)
+        lib_list = SelectField('library')
+        for lib in libraries:
+            lib_list.add_option(lib.name, lib.id)
+        widgets.append(dict(label='Library', 
+                            widget=lib_list, 
+                            helptext='Associated library where the resultant \
+                                        dataset will be stored'))
+        widgets = self.__create_form(trans, params, request_form_id, widgets, form_values)
+        title = 'Add a new request of type: %s' % request_type.name
+        return trans.fill_template( '/requests/new_request.mako',
+                        request_form_id=request_form_id,
+                        request_type=request_type,                                     
+                        widgets=widgets,
+                        title=title)
+        
+    def __create_form(self, trans, params, form_id, widgets=[], form_values=None):
+        form = trans.app.model.FormDefinition.get(form_id)
+        if not form_values:
+            values = {}
+            for field in form.fields:
+                if field['type'] in ['SelectField' or 'CheckBoxField']:
+                    values[field['label']] = False
+                else:
+                    values[field['label']] = ''
+        else:
+            values = form_values.content
+        # form fields
+        for field in form.fields:
+            fw = eval(field['type'])(field['label'])
+            if field['type'] == 'TextField':
+                fw.set_size(40)
+                fw.value = values[field['label']]
+            elif field['type'] == 'TextArea':
+                fw.set_size(3, 40)
+                fw.value = values[field['label']]
+            elif field['type'] == 'SelectField':
+                for option in field['selectlist']:
+                    fw.add_option(option, option, values[field['label']])
+            elif field['type'] == 'CheckBoxField':
+                fw.checked = values[field['label']]
+            
+            if field['required']:
+                req = 'Required'
+            else:
+                req = 'Optional'
+            widgets.append(dict(label=field['label'],
+                                widget=fw,
+                                helptext=field['helptext']+' ('+req+')'))
+        return widgets
+    @web.expose
+    def add_sample(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        request_id = int(util.restore_text( params.get( 'id', ''  ) ))
+        return self.__show_sample_form(trans, params, request_id)
+        
+    def __show_sample_form(self, trans, params, request_id, sample=None):
+        request = trans.app.model.Request.get(request_id)
+        request_type = trans.app.model.RequestType.get(request.request_type_id)
+        sample_form_id = request_type.sample_form_id
+        if sample:
+            form_values = trans.app.model.FormValues.get(sample.form_values_id)
+        else:
+            form_values = None
+        # list of widgets to be rendered on the request form
+        widgets = []
+        widgets.append(dict(label='Name', 
+                            widget=TextField('name'), 
+                            helptext='(Required)'))
+        widgets.append(dict(label='Description', 
+                            widget=TextField('desc'), 
+                            helptext='(Optional)'))
+        widgets[0]['widget'].set_size(40)
+        widgets[1]['widget'].set_size(40)
+        widgets = self.__create_form(trans, params, sample_form_id, widgets, form_values)
+        title = 'Add a new sample to request: %s of type: %s' % (request.name, request_type.name) 
+        return trans.fill_template( '/sample/new_sample.mako',
+                        sample_form_id=sample_form_id,
+                        request_id=request.id,                                     
+                        widgets=widgets,
+                        title=title)
+    @web.expose
+    def samples(self, trans, **kwd):
+        params = util.Params( kwd )
+        if params.get('save', False) == 'True':
+            sample = self.__save_sample(trans, params)
+            return trans.response.send_redirect( web.url_for( controller='requests',
+                                                              action='list',
+                                                              operation='samples',
+                                                              id=trans.security.encode_id(sample.request_id)) )
+    def __save_sample(self, trans, params, sample_id=None):
+        if not sample_id:
+            request = trans.app.model.Request.get(int(util.restore_text( params.request_id )))
+            request_type = trans.app.model.RequestType.get(request.request_type_id)
+            sample_form = trans.app.model.FormDefinition.get(request_type.sample_form_id)
+        else:
+            sample = trans.app.model.Sample.get(sample_id)
+            form_data = trans.app.model.FormData.get(sample.form_data_id)
+            form = trans.app.model.FormDefinition.get(form_data.form_definition_id)
+        name = params.get('name', '')
+        desc = params.get('desc', '')
+        values = {}
+        for field in sample_form.fields:
+            values[field['label']] = params.get(field['label'], '')
+        if not sample_id:
+            form_values = trans.app.model.FormValues(sample_form.id, values)
+            form_values.flush()
+            sample = trans.app.model.Sample(name, desc, request.id, form_values.id)
+            sample.flush()
+            # set the initial state            
+            state = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == request_type.id).first()
+            event = trans.app.model.SampleEvent(sample.id, state.id)
+            event.flush()
+        else:
+            form_data.content = values
+            form_data.flush()
+        return sample
+    def show_sample_read_only(self, trans, sample_id):
+        '''
+        Shows the sample details
+        '''
+        sample = trans.app.model.Sample.get(sample_id)
+        request = trans.app.model.Request.get(sample.request_id)
+        request_type = trans.app.model.RequestType.get(request.request_type_id)
+        sample_form = trans.app.model.FormDefinition.get(request_type.sample_form_id)
+        sample_values = trans.app.model.FormValues.get(sample.form_values_id)
+        # list of widgets to be rendered on the request form
+        sample_details = []
+        # main details
+        sample_details.append(dict(label='Name', 
+                                    value=sample.name, 
+                                    helptext=''))
+        sample_details.append(dict(label='Description', 
+                                    value=sample.desc, 
+                                    helptext=''))
+        sample_details.append(dict(label='Date created', 
+                                    value=sample.create_time, 
+                                    helptext=''))
+        sample_details.append(dict(label='Date updated', 
+                                    value=sample.create_time, 
+                                    helptext=''))
+        sample_details.append(dict(label='User', 
+                                    value=str(trans.user.email), 
+                                    helptext=''))
+        sample_details.append(dict(label='Request', 
+                                    value=request.name, 
+                                    helptext='Name/ID of the request this sample belongs to.'))
+        # get the current state of the sample
+        all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all()
+        curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+        sample_details.append(dict(label='State', 
+                                    value=curr_state.name, 
+                                    helptext=curr_state.desc))
+        # form fields
+        for field in sample_form.fields:
+            if field['required']:
+                req = 'Required'
+            else:
+                req = 'Optional'
+            sample_details.append(dict(label=field['label'],
+                                        value=sample_values.content[field['label']],
+                                        helptext=field['helptext']+' ('+req+')'))
+        return trans.fill_template( '/sample/view_sample.mako', 
+                                    sample_details=sample_details)
+    def show_events(self, trans, sample_id):
+        sample = trans.app.model.Sample.get(sample_id)
+        events_list = []
+        for event in trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all():
+            state = trans.app.model.SampleState.get(event.sample_state_id)
+            events_list.append((state.name, event.update_time, state.desc, event.comment))
+        return trans.fill_template( '/sample/sample_events.mako', 
+                                    events_list=events_list,
+                                    sample_name=sample.name,
+                                    request=trans.app.model.Request.get(sample.request_id).name)
+
+            
+    
+    
@@ -0,0 +1,315 @@
+from galaxy.web.base.controller import *
+from galaxy.web.framework.helpers import time_ago, iff, grids
+from galaxy.model.orm import *
+from galaxy.datatypes import sniff
+from galaxy import util
+from galaxy.util.streamball import StreamBall
+import logging, tempfile, zipfile, tarfile, os, sys
+from galaxy.web.form_builder import * 
+from datetime import datetime, timedelta
+
+log = logging.getLogger( __name__ )
+
+
+# States for passing messages
+SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
+
+class RequestsListGrid( grids.Grid ):
+    title = "Requests"
+    model_class = model.Request
+    default_sort_key = "-create_time"
+    columns = [
+        grids.GridColumn( "Name", key="name",
+                          link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ),
+                          attach_popup=True ),
+        grids.GridColumn( "Description", key="desc"),
+        grids.GridColumn( "Sample(s)", method='number_of_samples',
+                          link=( lambda item: iff( item.deleted, None, dict( operation="samples", id=item.id ) ) ), ),
+        grids.GridColumn( "Type", key="request_type_id", method='get_request_type'),
+        grids.GridColumn( "Last update", key="update_time", format=time_ago ),
+        grids.GridColumn( "User", key="user_id", method='get_user')
+        
+    ]
+    operations = [
+#        grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted )  ),
+        grids.GridOperation( "Samples", allow_multiple=False, condition=( lambda item: not item.deleted )  ),
+#        grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
+#        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),    
+    ]
+    standard_filters = [
+        grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
+        grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
+        grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
+    ]
+    def get_user(self, trans, request):
+        return trans.app.model.User.get(request.user_id).email
+    def get_current_item( self, trans ):
+        return None
+    def get_request_type(self, trans, request):
+        request_type = trans.app.model.RequestType.get(request.request_type_id)
+        return request_type.name
+    def apply_default_filter( self, trans, query ):
+        return query
+    def number_of_samples(self, trans, request):
+        return str(len(trans.app.model.Sample.filter(trans.app.model.Sample.table.c.request_id==request.id).all()))
+    
+class SamplesListGrid( grids.Grid ):
+    model_class = model.Sample
+    default_sort_key = "-create_time"
+    columns = [
+        grids.GridColumn( "Name", key="name",
+                          link=( lambda item: iff( item.deleted, None, dict( operation="show_sample", id=item.id ) ) ),
+                          attach_popup=True ),
+        grids.GridColumn( "Description", key='desc' ),
+        grids.GridColumn( "Status", method="get_status",
+                          link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) )),
+
+        grids.GridColumn( "Last update", key="update_time", format=time_ago )
+        
+        # Valid for filtering but invisible
+        #grids.GridColumn( "Deleted", key="deleted", visible=False )
+    ]
+    operations = [
+#        grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted )  ),
+        grids.GridOperation( "Change state", condition=( lambda item: not item.deleted )  ),
+#        grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
+#        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),
+        
+    ]
+    standard_filters = [
+        grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
+        grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
+        grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
+    ]
+    def __init__(self, request, user):
+        self.request  = request
+        self.user = user
+    def get_current_item( self, trans ):
+        return None
+    def apply_default_filter( self, trans, query ):
+        return query.filter_by( request_id=self.request.id )
+    def get_status(self, trans, sample):
+        all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all()
+        curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+        return curr_state.name
+
+class Requests( BaseController ):
+    request_grid = RequestsListGrid()
+    
+    @web.expose
+    @web.require_admin
+    def index( self, trans ):
+        return trans.fill_template( "/admin/requests/index.mako" )
+    def get_authorized_libs(self, trans):
+        all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all()
+        authorized_libraries = []
+        for library in all_libraries:
+            if trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library) or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library) or trans.app.security_agent.check_folder_contents(trans.user, library) or trans.app.security_agent.show_library_item(trans.user, library):
+                authorized_libraries.append(library)
+        return authorized_libraries
+    @web.expose
+    @web.require_admin
+    def list( self, trans, **kwargs ):
+        '''
+        List all request made by the current user
+        '''
+        status = message = None
+        if 'operation' in kwargs:
+            operation = kwargs['operation'].lower()
+            if operation == "show_request":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.show_read_only(trans, id)
+            elif operation == "samples":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.show_samples(trans, id, kwargs)
+            elif operation == "show_sample":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.show_sample_read_only(trans, id)
+            elif operation == "change state":
+                id_list = [trans.security.decode_id(id) for id in util.listify(kwargs['id'])]
+                return self.change_state(trans, id_list)
+            elif operation == "events":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.show_events(trans, id)
+        # Render the list view
+        return self.request_grid( trans, status=status, message=message, template='/admin/requests/grid.mako', **kwargs )
+    def show_samples(self, trans, id, kwargs):
+        '''
+        Shows all the samples associated with this request
+        '''
+        status = message = None
+        request = trans.app.model.Request.get(id)
+        self.samples_grid = SamplesListGrid(request, trans.app.model.User.get(request.user_id))
+        return self.samples_grid( trans, status=status, message=message, template='/admin/samples/grid.mako', **kwargs )        
+    def show_read_only(self, trans, id):
+        '''
+        Shows the request details
+        '''
+        request = trans.app.model.Request.get(id)
+        request_type = trans.app.model.RequestType.get(request.request_type_id)
+        request_form = trans.app.model.FormDefinition.get(request_type.request_form_id)
+        request_values = trans.app.model.FormValues.get(request.form_values_id)
+        libraries = self.get_authorized_libs(trans)
+        # list of widgets to be rendered on the request form
+        request_details = []
+        # main details
+        request_details.append(dict(label='Name', 
+                                    value=request.name, 
+                                    helptext=''))
+        request_details.append(dict(label='Description', 
+                                    value=request.desc, 
+                                    helptext=''))
+        request_details.append(dict(label='Type', 
+                                    value=request_type.name, 
+                                    helptext=''))
+        request_details.append(dict(label='Date created', 
+                                    value=request.create_time, 
+                                    helptext=''))
+        request_details.append(dict(label='Date updated', 
+                                    value=request.create_time, 
+                                    helptext=''))
+        request_details.append(dict(label='User', 
+                                    value=str(trans.user.email), 
+                                    helptext=''))
+        # library associated
+        request_details.append(dict(label='Library', 
+                            value=trans.app.model.Library.get(request.library_id).name, 
+                            helptext='Associated library where the resultant \
+                                        dataset will be stored'))
+        # form fields
+        for field in request_form.fields:
+            if field['required']:
+                req = 'Required'
+            else:
+                req = 'Optional'
+            request_details.append(dict(label=field['label'],
+                                        value=request_values.content[field['label']],
+                                        helptext=field['helptext']+' ('+req+')'))
+        return trans.fill_template( '/admin/requests/view_request.mako',
+                                    request_form_id=request_form.id, 
+                                    request_details=request_details,
+                                    request_type=request_type)    
+
+    @web.expose
+    @web.require_admin
+    def samples(self, trans, **kwd):
+        params = util.Params( kwd )
+        if params.get('save', False) == 'True':
+            sample = self.__save_sample(trans, params)
+            return self.show_samples(trans, sample.request_id, {})            
+    def show_sample_read_only(self, trans, sample_id):
+        '''
+        Shows the sample details
+        '''
+        sample = trans.app.model.Sample.get(sample_id)
+        request = trans.app.model.Request.get(sample.request_id)
+        request_type = trans.app.model.RequestType.get(request.request_type_id)
+        sample_form = trans.app.model.FormDefinition.get(request_type.sample_form_id)
+        sample_values = trans.app.model.FormValues.get(sample.form_values_id)
+        # list of widgets to be rendered on the request form
+        sample_details = []
+        # main details
+        sample_details.append(dict(label='Name', 
+                                    value=request.name, 
+                                    helptext=''))
+        sample_details.append(dict(label='Description', 
+                                    value=request.desc, 
+                                    helptext=''))
+        sample_details.append(dict(label='Date created', 
+                                    value=sample.create_time, 
+                                    helptext=''))
+        sample_details.append(dict(label='Date updated', 
+                                    value=sample.create_time, 
+                                    helptext=''))
+        sample_details.append(dict(label='User', 
+                                    value=str(trans.user.email), 
+                                    helptext=''))
+        sample_details.append(dict(label='Request', 
+                                    value=request.name, 
+                                    helptext='Name/ID of the request this sample belongs to.'))
+        # get the current state of the sample
+        all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).all()
+        curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+        sample_details.append(dict(label='State', 
+                                    value=curr_state.name, 
+                                    helptext=curr_state.desc))
+        # form fields
+        for field in sample_form.fields:
+            if field['required']:
+                req = 'Required'
+            else:
+                req = 'Optional'
+            sample_details.append(dict(label=field['label'],
+                                        value=sample_values.content[field['label']],
+                                        helptext=field['helptext']+' ('+req+')'))
+        return trans.fill_template( '/admin/samples/view_sample.mako', 
+                                    sample_details=sample_details)
+    def __get_all_states(self, trans, sample):
+        request = trans.app.model.Request.get(sample.request_id)
+        request_type = trans.app.model.RequestType.get(request.request_type_id)
+        all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all()
+        curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+        states_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == request_type.id)
+        return states_list
+    def __get_curr_state(self, trans, sample):
+        all_states = trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample.id).all()
+        curr_state = trans.app.model.SampleState.get(all_states[len(all_states)-1].sample_state_id)
+        return curr_state
+    def change_state(self, trans, sample_id_list):
+        sample = trans.app.model.Sample.get(sample_id_list[0])
+        states_list = self.__get_all_states(trans, sample)
+        curr_state = self.__get_curr_state(trans, sample)
+        states_input = SelectField('select_state')
+        for state in states_list:
+            if len(sample_id_list) == 1:
+                if curr_state.name == state.name:
+                    states_input.add_option(state.name+' (Current)', state.name, selected=True)
+                else:
+                    states_input.add_option(state.name, state.name)
+            else:
+                states_input.add_option(state.name, state.name)
+        widgets = []
+        widgets.append(('Select the new state of the sample(s) from the list of possible state(s)',
+                      states_input))
+        widgets.append(('Comments', TextArea('comment')))
+        title = 'Change current state of sample: ' + sample.name
+        return trans.fill_template( '/admin/samples/change_state.mako', 
+                                    widgets=widgets, title=title, 
+                                    sample_id_list=util.object_to_string(sample_id_list)) 
+    @web.expose
+    @web.require_admin
+    def save_state(self, trans, **kwd):
+        params = util.Params( kwd )
+        sample_id_list = util.string_to_object(util.restore_text( params.sample_id_list ))
+        comments = util.restore_text( params.comment )
+        sample = trans.app.model.Sample.get(sample_id_list[0])
+        request = trans.app.model.Request.get(sample.request_id)
+        selected_state = util.restore_text( params.select_state )
+        new_state = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == request.request_type_id 
+                                                        and trans.app.model.SampleState.table.c.name == selected_state)[0]
+        for sample_id in sample_id_list:
+            event = trans.app.model.SampleEvent(sample_id, new_state.id, comments)
+            event.flush()
+        return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                          action='list',
+                                                          operation='samples',
+                                                          id=trans.security.encode_id(request.id)) )
+    @web.expose
+    @web.require_admin
+    def show_events(self, trans, sample_id):
+        sample = trans.app.model.Sample.get(sample_id)
+        request = trans.app.model.Request.get(sample.request_id)
+        events_list = []
+        for event in trans.app.model.SampleEvent.filter(trans.app.model.SampleEvent.table.c.sample_id == sample_id).order_by(trans.app.model.SampleEvent.c.update_time.desc()).all():
+            state = trans.app.model.SampleState.get(event.sample_state_id)
+            delta = datetime.utcnow() - event.update_time
+            if delta > timedelta( minutes=60 ):
+                last_update = '%s hours' % int( delta.seconds / 60 / 60 )
+            else:
+                last_update = '%s minutes' % int( delta.seconds / 60 )
+            events_list.append((state.name, state.desc, last_update, event.comment))
+        return trans.fill_template( '/admin/samples/events.mako', 
+                                    events_list=events_list,
+                                    sample_name=sample.name, user=trans.app.model.User.get(request.user_id),
+                                    request=request.name)
+    
@@ -9,6 +9,11 @@ class BaseField(object):
    def get_html( self, prefix="" ):
        """Returns the html widget corresponding to the parameter"""
        raise TypeError( "Abstract Method" )
+    @staticmethod
+    def form_field_types():
+        return ['TextField', 'TextArea', 'SelectField', 'CheckboxField']
+        
+        
        
 class TextField(BaseField):
    """
@@ -26,6 +31,8 @@ class TextField(BaseField):
    def get_html( self, prefix="" ):
        return '<input type="text" name="%s%s" size="%d" value="%s">' \
            % ( prefix, self.name, self.size, self.value )
+    def set_size(self, size):
+        self.size = int( size )

 class TextArea(BaseField):
    """
@@ -45,6 +52,9 @@ class TextArea(BaseField):
    def get_html( self, prefix="" ):
        return '<textarea name="%s%s" rows="%d" cols="%d">%s</textarea>' \
            % ( prefix, self.name, self.rows, self.cols, self.value )
+    def set_size(self, rows, cols):
+        self.rows = rows
+        self.cols = cols

 class CheckboxField(BaseField):
    """
@@ -215,6 +225,17 @@ class SelectField(BaseField):
        rval.insert( 0, '<select name="%s%s"%s%s%s>' % ( prefix, self.name, multiple, self.refresh_on_change_text, last_selected_value ) )
        rval.append( '</select>' )
        return "\n".join( rval )
+    def get_selected(self):
+        '''
+        This method returns the currently selected option's text and value
+        '''
+        for text, value, selected in self.options:
+            if selected:
+                return text, value
+        if self.options:
+            return self.options[0]
+        return None
+            


 class DrillDownField( BaseField ):
@@ -607,6 +607,11 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
            if dbkey == ds.dbkey:
                return ds
        return None
+    
+    def request_types(self):
+        if self.app.model.RequestType.query().all():
+            return True
+        return False
        
 class FormBuilder( object ):
    """
@@ -0,0 +1,31 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Create a new form definition</div>
+    <div class="toolFormBody">
+        <form name="create_form" action="${h.url_for( controller='forms', action='new', create_form=True, new=False, create_fields=False  )}" method="post" >
+            %for label, input in inputs:
+                <div class="form-row">
+                    <label>${label}</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        ${input.get_html()}
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+            %endfor
+            <div class="form-row">
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="hidden" name="new" value="submitted" size="40"/>
+                </div>
+              <div style="clear: both"></div>
+            </div>
+            <input type="submit" name="save_form" value="Save"/>
+        </form>
+    </div>
+</div>
@@ -0,0 +1,105 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<script type="text/javascript">
+$( function() {
+    $( "select[refresh_on_change='true']").change( function() {
+        var refresh = false;
+        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+        if ( refresh_on_change_values ) {
+            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+            for( i= 0; i < refresh_on_change_values.length; i++ ) {
+                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+                    refresh = true;
+                    break;
+                }
+            }
+        }
+        else {
+            refresh = true;
+        }
+        if ( refresh ){
+            $( "#edit_form" ).submit();
+        }
+    });
+});
+</script>
+
+<%def name="render_selectbox_options( index, field_attr )">
+    %if field_attr[0] == 'Type':
+        %if field_attr[1].get_selected()[0] == 'SelectField':
+            <% options = field_attr[2] %>
+            <div class="repeat-group-item">
+                <label> Options</label>
+                %for i, option in enumerate(options):
+                    <b> ${i+1}</b>
+                    ${option[1].get_html()}
+                    ##<input type="submit" name="remove_option_${index}" value="Remove option ${i+1}"/><br>
+                    <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='remove', field_index=index, option_index=i )}">Remove</a><br>
+                %endfor
+           </div>
+            <div class="form-row">
+                <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='add', field_index=index )}">Add</a>
+            </div>
+            ##<div class="form-row">
+            ##    <input type="submit" name="add_option_field_${index}" value="Add option"/>
+            ##</div>
+        %endif
+    %endif
+</%def>
+
+
+<%def name="render_field( index, field )">
+    <div class="repeat-group-item">
+        <div class="form-row">
+            <label>Field ${1+index}</label>
+        </div>
+        %for field_attr in field:
+            <div class="form-row">
+                <label>${field_attr[0]}</label>
+                ${field_attr[1].get_html()}
+                ${render_selectbox_options( index, field_attr )}
+            </div>
+        %endfor
+        <div class="form-row">
+            <input type="submit" name="remove_button" value="Remove field ${index+1}"/>
+        </div>
+   </div>
+</%def>
+
+<div class="toolForm">
+    <div class="toolFormTitle">Edit form definition '${form.name}'</div>
+    <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id, num_fields=len(form.fields)  )}" method="post" >
+        %for label, input in form_details:
+            <div class="form-row">
+                <label>${label}</label>
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    ${input.get_html()}
+                </div>
+                <div style="clear: both"></div>
+            </div>
+        %endfor
+        <div class="toolFormTitle">Sample fields (${len(form.fields)})</div>
+        %for ctr, field in enumerate(field_details):
+            ${render_field( ctr, field )}
+        %endfor
+        <div class="form-row">
+            <input type="submit" name="add_field_button" value="Add field"/>
+        </div>
+        <div class="form-row">
+            <div style="float: left; width: 250px; margin-right: 10px;">
+                <input type="hidden" name="refresh" value="true" size="40"/>
+            </div>
+          <div style="clear: both"></div>
+        </div>
+        <input type="submit" name="save_changes_button" value="Save"/>
+    </form>
+    </div>
+</div>
@@ -0,0 +1,73 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+<%def name="title()">Manage Form Definitions</%def>
+
+## Render a row
+<%def name="render_row( form, ctr )">
+    %if ctr % 2 == 1:
+        <tr class="odd_row">
+    %else:
+        <tr>
+    %endif
+        <td>
+            <b><a href="${h.url_for( controller='forms', action='edit', form_id=form.id, read_only=True )}">${form.name}</a></b>
+            <a id="form-${form.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
+            <div popupmenu="form-${form.id}-popup">
+                <a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit form definition</a>
+            </div>
+        </td>
+        <td><i>${form.desc}</i></td>
+    </tr>
+</%def>
+
+
+<h2>
+    %if deleted:
+        Deleted 
+    %endif
+    Forms
+</h2>
+
+
+
+<ul class="manage-table-actions">
+    %if not deleted:
+        <li>
+            <a class="action-button" href="${h.url_for( controller='forms', action='new', new=True )}">
+            <img src="${h.url_for('/static/images/silk/add.png')}" />
+            <span>Define a new form</span></a>
+        </li>
+    %endif
+</ul>
+
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+%if not fdc_list:
+    %if deleted:
+        There are no deleted forms
+    %else:
+        There are no forms.
+    %endif
+%else:
+    <table class="grid">
+        <thead>
+            <tr>
+                <th>Name</th>
+                <th>Description</th>
+            </tr>
+        </thead>
+        <tbody>
+            %for ctr, fdc in enumerate( fdc_list ):    
+                <tr>
+                ${render_row( fdc.latest_form, ctr )}
+                </tr>          
+            %endfor
+        </tbody>
+    </table>
+%endif
@@ -0,0 +1,67 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">${form.name} - <i>${form.desc}</i></div>
+    <form name="library" action="${h.url_for( controller='forms', action='manage' )}" method="post" >
+        <table class = "grid">
+            <tbody>
+                %for index, field in enumerate(form.fields):
+                    <tr>
+                        <td>
+                            <div class="form-row">
+                                <label>${1+index}. Label</label>
+                                <a>${field['label']}</a>
+                                %if field['type'] == 'SelectField':
+                                    <a id="${field['label']}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
+                                    %for option in field['selectlist']:
+                                        <div popupmenu="${field['label']}-type-popup">
+                                            <a class="action-button" href="" >${option}</a>
+                                        </div>                                 
+                                    %endfor
+                                %endif                                    
+                            </div>
+                        </td>
+                        <td>
+                            <div class="form-row">
+                                <label>Help text </label>
+                                %if not field['helptext']:
+                                    <a><i>No helptext</i></a>
+                                %else:
+                                    <a>${field['helptext']}</a>
+                                %endif
+                            </div>
+                        </td>                            
+                        <td>
+                            <div class="form-row">
+                                <label>Type:</label>
+                                <a>${field['type']}</a>
+                                %if field['type'] == 'SelectField':
+                                    <a id="fieldtype-popup" class="popup-arrow" style="display: none;">&#9660;</a>
+                                    %for option in field['selectlist']:
+                                        <div popupmenu="type-popup">
+                                            <a class="action-button" href="" >${option}</a>
+                                        </div>                                 
+                                    %endfor
+                                %endif
+                            </div>
+                        </td>
+                        <td>
+                            <div class="form-row">
+                                <label>Required?</label>
+                                <a>${field['required']}</a>
+                            </div>
+                        </td>
+                    </tr>       
+                %endfor
+            </tbody>
+        </table>            
+        ##<input type="submit" name="save_changes_button" value="Back"/>
+    </form>
+    </div>
+</div>
@@ -103,13 +103,35 @@
                    <div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div>
                  </div>
                </div>
+                <div class="toolSectionPad"></div>
+                <div class="toolSectionTitle">
+                  <span>Forms</span>
+                </div>
+                <div class="toolSectionBody">
+                  <div class="toolSectionBg">
+                    <div class="toolTitle"><a href="${h.url_for( controller='forms', action='manage' )}" target="galaxy_main">Manage forms</a></div>
+                  </div>
+                </div>
+                <div class="toolSectionPad"></div>
+                <div class="toolSectionTitle">
+                  <span>Requests</span>
+                </div>
+                <div class="toolSectionBody">
+                  <div class="toolSectionBg">
+                    <div class="toolTitle"><a href="${h.url_for( controller='admin', action='manage_request_types' )}" target="galaxy_main">Manage request types</a></div>
+                    <div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='list')}" target="galaxy_main">Manage requests</a></div>
+                  </div>
+                </div>
            </div>
        </div>    
    </div>
+    ##<iframe name="galaxy_admin" src="${h.url_for( controller='admin', action='index' )}" frameborder="0" style="position: absolute; margin: 0; border: 0 none; height: 100%; width: 100%;"> </iframe>
 </%def>

 <%def name="center_panel()">
-
-    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( action='center' )}"> </iframe>
+    <%
+        center_url = h.url_for( action='center' )
+    %>
+    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe>

 </%def>
@@ -0,0 +1,26 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Create ${num_states} states for the '${sample_type_name}' sample type</div>
+    <form name="new_form_fields" action="${h.url_for( controller='admin', action='request_type', save_new=True, create=False, edit=False, name=sample_type_name, description=desc, num_states=num_states, request_form_id=request_form_id, sample_form_id=sample_form_id)}" method="post" >
+        <div class="toolFormBody">
+            %for element_count in range( num_states ):
+                <div class="form-row">
+                    <label>${1+element_count}) State name:</label>
+                    <input type="text" name="new_element_name_${element_count}" value="" size="40"/>
+                    <label>State help text (optional):</label>
+                    <input type="text" name="new_element_description_${element_count}" value="" size="40"/>
+                </div>
+                <div style="clear: both"></div>
+            %endfor
+        </div>
+        <div class="toolFormBody">
+            <input type="submit" name="save_new_sample_type" value="Save"/>
+        </div>
+    </form>
+</div>
@@ -0,0 +1,66 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Create a new request type</div>
+    %if not forms:
+        Create a form definition first to create a new request type.
+    %else:
+        <div class="toolFormBody">
+            <form name="create_request_type" action="${h.url_for( controller='admin', action='request_type', add_states=True, create=False, edit=False  )}" method="post" >
+                <div class="form-row">
+                    <label>Name:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <input type="text" name="name" value="New Request Type" size="40"/>
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>Description:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <input type="text" name="description" value="" size="40"/>
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+                <div class="form-row">
+                    <label>
+                        Request Form definition:
+                    </label>
+                    <select name="request_form_id">
+                        %for form in forms:
+                            <option value="${form.id}">${form.name}</option>
+                        %endfor
+                    </select>
+                </div>
+                <div class="form-row">
+                    <label>
+                        Sample Form definition:
+                    </label>
+                    <select name="sample_form_id">
+                        %for form in forms:
+                            <option value="${form.id}">${form.name}</option>
+                        %endfor
+                    </select>
+                </div>
+                <div class="form-row">
+                    <label>Number of sample states:</label>
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <input type="text" size="3" name="num_states" value="1"/> 
+                    </div>
+                </div>           
+                <div class="form-row">
+                    <div style="float: left; width: 250px; margin-right: 10px;">
+                        <input type="hidden" name="new" value="submitted" size="40"/>
+                    </div>
+                  <div style="clear: both"></div>
+                </div>
+                <input type="submit" name="create_library_button" value="Define states"/>
+            </form>
+        </div>
+    %endif
+</div>
@@ -0,0 +1,78 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<% num_states=len(states_list) %>
+
+<div class="toolForm">
+    <div class="toolFormTitle">Edit the request type</div>
+    <div class="toolFormBody">
+        <form name="library" action="${h.url_for( controller='admin', action='request_type', save_changes=True, create=False, id=request_type.id, num_states=num_states )}" method="post" >
+            <div class="form-row">
+                <label>Name:</label>
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="text" name="name" value="${request_type.name}" size="40"/>
+                </div>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Description:</label>
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="text" name="description" value="${request_type.desc}" size="40"/>
+                </div>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>
+                    Request Form definition: 
+                </label>
+                <select name="form_id">
+                    %for form in forms:
+                        %if form.id == request_type.request_form_id:
+                            <option value="${form.id}" selected>${form.name}</option>
+                        %else:
+                            <option value="${form.id}">${form.name}</option>
+                        %endif
+                    %endfor
+                </select>
+            </div>       
+            <div class="form-row">
+                <label>
+                    Sample Form definition: 
+                </label>
+                <select name="form_id">
+                    %for form in forms:
+                        %if form.id == request_type.sample_form_id:
+                            <option value="${form.id}" selected>${form.name}</option>
+                        %else:
+                            <option value="${form.id}">${form.name}</option>
+                        %endif
+                    %endfor
+                </select>
+            </div>    
+            <div class="toolFormBody">
+                %for element_count, state in enumerate(states_list):
+                    <div class="form-row">
+                        <label>${1+element_count}) State name:</label>
+                        <input type="text" name="new_element_name_${element_count}" value="${state.name}" size="40"/>
+                        <label>State help text (optional):</label>
+                        <input type="text" name="new_element_description_${element_count}" value="${state.desc}" size="40"/>
+                    </div>
+                    <div style="clear: both"></div>
+                %endfor
+            </div>
+            <div class="form-row">
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="hidden" name="new" value="submitted" size="40"/>
+                </div>
+              <div style="clear: both"></div>
+            </div>
+
+            <input type="submit" name="edit_request_type_button" value="Save"/>
+        </form>
+    </div>
+</div>
@@ -0,0 +1,205 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Browse Requests</%def>
+
+%if message:
+    <p>
+        <div class="${message_type}message transient-message">${message}</div>
+        <div style="clear: both"></div>
+    </p>
+%endif
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    <script type="text/javascript">        
+        ## TODO: generalize and move into galaxy.base.js
+        $(document).ready(function() {
+            $(".grid").each( function() {
+                var grid = this;
+                var checkboxes = $(this).find("input.grid-row-select-checkbox");
+                var update = $(this).find( "span.grid-selected-count" );
+                $(checkboxes).each( function() {
+                    $(this).change( function() {
+                        var n = $(checkboxes).filter("[checked]").size();
+                        update.text( n );
+                    });
+                })
+            });
+        });
+        ## Can this be moved into base.mako?
+        %if refresh_frames:
+            %if 'masthead' in refresh_frames:            
+                ## Refresh masthead == user changes (backward compatibility)
+                if ( parent.user_changed ) {
+                    %if trans.user:
+                        parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} );
+                    %else:
+                        parent.user_changed( null, false );
+                    %endif
+                }
+            %endif
+            %if 'history' in refresh_frames:
+                if ( parent.frames && parent.frames.galaxy_history ) {
+                    parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}";
+                    if ( parent.force_right_panel ) {
+                        parent.force_right_panel( 'show' );
+                    }
+                }
+            %endif
+            %if 'tools' in refresh_frames:
+                if ( parent.frames && parent.frames.galaxy_tools ) {
+                    parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}";
+                    if ( parent.force_left_panel ) {
+                        parent.force_left_panel( 'show' );
+                    }
+                }
+            %endif
+        %endif
+    </script>
+</%def>
+
+<%def name="stylesheets()">
+    <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
+    <style>
+        ## Not generic to all grids -- move to base?
+        .count-box {
+            min-width: 1.1em;
+            padding: 5px;
+            border-width: 1px;
+            border-style: solid;
+            text-align: center;
+            display: inline-block;
+        }
+    </style>
+</%def>
+
+<div class="grid-header">
+    <h2>${grid.title}</h2>
+    %if len(query.all()):
+        <h3>All Users</h3>
+    %endif
+##    %if len(query.all()):
+##        <span class="title">Filter:</span>
+##        %for i, filter in enumerate( grid.standard_filters ):
+##            %if i > 0:    
+##                <span>|</span>
+##            %endif
+##            <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span>
+##        %endfor
+##    %endif
+</div>
+
+
+%if not len(query.all()):
+    There are no request(s).
+%else:
+<form name="history_actions" action="${url()}" method="post" >
+    <table class="grid">
+        <thead>
+            <tr>
+                <th></th>
+                %for column in grid.columns:
+                    %if column.visible:
+                        <%
+                            href = ""
+                            extra = ""
+                            if column.sortable:
+                                if sort_key == column.key:
+                                    if sort_order == "asc":
+                                        href = url( sort=( "-" + column.key ) )
+                                        extra = "&darr;"
+                                    else:
+                                        href = url( sort=( column.key ) )
+                                        extra = "&uarr;"
+                                else:
+                                    href = url( sort=column.key )
+                        %>
+                        <th\
+                        %if column.ncells > 1:
+                            colspan="${column.ncells}"
+                        %endif
+                        >
+                            %if href:
+                                <a href="${href}">${column.label}</a>
+                            %else:
+                                ${column.label}
+                            %endif
+                            <span>${extra}</span>
+                        </th>
+                    %endif
+                %endfor
+                <th></th>
+            </tr>
+        </thead>
+        <tbody>
+            %for i, item in enumerate( query ):
+                <tr \
+                %if current_item == item:
+                    class="current" \
+                %endif
+                > 
+                    ## Item selection column
+                    <td style="width: 1.5em;">
+                        <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" />
+                    </td>
+                    ## Data columns
+                    %for column in grid.columns:
+                        %if column.visible:
+                            <%
+                                # Link
+                                if column.link and column.link( item ):
+                                    href = url( **column.link( item ) )
+                                else:
+                                    href = None
+                                # Value (coerced to list so we can loop)
+                                value = column.get_value( trans, grid, item )
+                                if column.ncells == 1:
+                                    value = [ value ]
+                            %>
+                            %for cellnum, v in enumerate( value ):
+                                <%
+                                    # Attach popup menu?
+                                    if column.attach_popup and cellnum == 0:
+                                        extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">&#9660;</a>' % i
+                                    else:
+                                        extra = ""
+                                %>
+                                %if href:                    
+                                    <td><a href="${href}">${v}</a>&nbsp;${extra}</td>
+                                %else:
+                                    <td >${v}${extra}</td>
+                                %endif    
+                                </td>
+                            %endfor
+                        %endif
+                    %endfor
+                    ## Actions column
+                    <td>
+                        <div popupmenu="grid-${i}-popup">
+                            %for operation in grid.operations:
+                                %if operation.allowed( item ):
+                                    <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a>
+                                %endif
+                            %endfor
+                        </div>
+                    </td>
+                </tr>
+            %endfor
+        </tbody>
+##        <tfoot>
+##            <tr>
+##                <td></td>
+##                <td colspan="100">
+##                    For <span class="grid-selected-count"></span> selected requests:
+##                    %for operation in grid.operations:
+##                        %if operation.allow_multiple:
+##                            <input type="submit" name="operation" value="${operation.label}" class="action-button">
+##                        %endif
+##                    %endfor
+##                </td>
+##            </tr>
+##        </tfoot>
+    </table>
+</form>
+%endif
@@ -0,0 +1,60 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">request Types</%def>
+
+<h2>
+    %if deleted:
+        Deleted 
+    %endif
+    Request Types
+</h2>
+
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button" href="${h.url_for( controller='admin', action='request_type', create=True )}"><span>Create a new request type</span></a>
+    </li>
+</ul>
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+%if not request_types:
+    %if deleted:
+        There are no deleted request types
+    %else:
+        There are no request types.
+    %endif
+%else:
+    <table class="grid">
+        <thead>
+            <tr>
+                <th>Name</th>
+                <th>Description</th>
+                <th>Request Form</th>
+                <th>Sample Form</th>
+            </tr>
+        </thead>
+        <tbody>
+            %for request_type in request_types:    
+                <tr>
+                    <td><b><a href="${h.url_for( controller='admin', action='request_type', edit='True', id=request_type.id)}">${request_type.name}</a></b></td>
+                    <td><i>${request_type.desc}</i></td>
+                    <%  for form in forms:
+                            if form.id == request_type.request_form_id:
+                                form_name = form.name
+                                break
+                    %>
+                    <td><a href="${h.url_for( controller='forms', action='edit', form_id=request_type.request_form_id, read_only=True)}">${form_name}</a></td>
+                    <%  for form in forms:
+                            if form.id == request_type.sample_form_id:
+                                form_name = form.name
+                                break
+                    %>
+                    <td><a href="${h.url_for( controller='forms', action='edit', form_id=request_type.sample_form_id, read_only=True)}">${form_name}</a></td> 
+               </tr>          
+            %endfor
+        </tbody>
+    </table>
+%endif
@@ -0,0 +1,20 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Request Details: '${request_details[0]['value']}'</div>
+        %for index, rd in enumerate(request_details):
+            <div class="form-row">
+                <label>${rd['label']}</label>
+                ##<i>${rd['helptext']}</i>                                   
+                ${rd['value']}
+            </div>
+            <div style="clear: both"></div>
+        %endfor
+    </div>
+</div>
@@ -0,0 +1,30 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+<div class="toolForm">
+    <div class="toolFormTitle">${title}</div>
+    <div class="toolFormBody">
+        <form name="event" action="${h.url_for( controller='requests_admin', action='save_state', new=True, sample_id_list=sample_id_list)}" method="post" >
+                %for w in widgets:
+                    <div class="form-row">
+                        <label>
+                            ${w[0]}
+                        </label>
+                        ${w[1].get_html()}
+                        %if w[0] == 'Comments':
+                            <div class="toolParamHelp" style="clear: both;">
+                                Optional
+                            </div>
+                        %endif
+                    </div>
+                %endfor
+            <div class="form-row">
+                <input type="submit" name="add_event" value="Save"/>
+            </div>
+        </form>
+    </div>
+</div>
@@ -0,0 +1,83 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Edit sample named: ${values.content['Name']}</div>
+    <div class="toolFormBody">
+        <form name="sample" action="${h.url_for( controller='sample', action='do', save_changes=True, sample_id=sample.id )}" method="post" >
+            <div class="form-row">
+                <label>
+                    Library:
+                </label>
+                <select name="library_id">
+                    %for library in libraries:
+                        <option value="${library.id}">${library.name}</option>
+                    %endfor
+                </select>
+            </div>
+            %for i, field in enumerate(form.fields):
+                <div class="form-row">
+                    <label>${field['label']}</label>
+                    %if field['type'] == 'TextField':
+                        <input type="text" name="${field['label']}" value="${values.content[field['label']]}" size="40"/>
+                    %elif field['type'] == 'TextArea':
+                        <textarea name="${field['label']}" rows="3" cols="35">${values.content[field['label']]}</textarea>
+                    %elif field['type'] == 'CheckBox':
+                        %if values.content[field['label']] == "true":
+                            <input type="checkbox" name="${field['label']}" value="true" checked>
+                        %else:
+                            <input type="checkbox" name="${field['label']}" value="true">
+                        %endif
+                    %elif field['type'] == 'SelectBox':
+                        <select name="${field['label']}">
+                            %for ft in field['selectlist']:
+                                %if ft == values.content[field['label']]:
+                                    <option value="${ft}" selected>${ft}</option>
+                                %else:
+                                    <option value="${ft}">${ft}</option>
+                                %endif
+                            %endfor
+                        </select>
+                    %endif
+                    <div class="toolParamHelp" style="clear: both;">
+                    ${field['helptext']}
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+            %endfor                    
+            <div class="form-row">
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="hidden" name="new" value="submitted" size="40"/>
+                </div>
+              <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <input type="submit" name="create_library_button" value="Save"/>
+            </div>
+        </form>
+    </div>
+</div>
+<div class="toolForm">
+    <div class="toolFormBody">
+        <form name="event" action="${h.url_for( controller='admin', action='event', new=True, sample_id=sample.id)}" method="post" >
+            <div class="form-row">
+                <label>
+                    Change sample state to:
+                </label>
+                <select name="state_id">
+                    %for state in states:
+                        <option value="${state.id}">${state.name}</option>
+                    %endfor
+                </select>
+            </div>
+            <div class="form-row">
+                <input type="submit" name="add_event" value="Save"/>
+            </div>
+        </form>
+    </div>
+</div>
@@ -0,0 +1,33 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Events for Sample ${sample_name}</%def>
+
+<h2>Events for Sample "${sample_name}" of Request: ${request}</h2>
+<h3>User: ${user.email}</h3>
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+
+<table class="grid">
+    <thead>
+        <tr>
+            <th>State</th>
+            <th>Description</th>
+            <th>Last Update</th>
+            <th>Comments</th>
+        </tr>
+    </thead>
+    <tbody>
+        %for state, desc, updated, comments in events_list:    
+            <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
+                <td><b><a>${state}</a></b></td>
+                <td><a>${desc}</a></td>
+                <td><a>${updated}</a></td>
+                <td><a>${comments}</a></td>
+            </tr>             
+        %endfor
+    </tbody>
+</table>
@@ -0,0 +1,203 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Browse Samples</%def>
+
+%if message:
+    <p>
+        <div class="${message_type}message transient-message">${message}</div>
+        <div style="clear: both"></div>
+    </p>
+%endif
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    <script type="text/javascript">        
+        ## TODO: generalize and move into galaxy.base.js
+        $(document).ready(function() {
+            $(".grid").each( function() {
+                var grid = this;
+                var checkboxes = $(this).find("input.grid-row-select-checkbox");
+                var update = $(this).find( "span.grid-selected-count" );
+                $(checkboxes).each( function() {
+                    $(this).change( function() {
+                        var n = $(checkboxes).filter("[checked]").size();
+                        update.text( n );
+                    });
+                })
+            });
+        });
+        ## Can this be moved into base.mako?
+        %if refresh_frames:
+            %if 'masthead' in refresh_frames:            
+                ## Refresh masthead == user changes (backward compatibility)
+                if ( parent.user_changed ) {
+                    %if trans.user:
+                        parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} );
+                    %else:
+                        parent.user_changed( null, false );
+                    %endif
+                }
+            %endif
+            %if 'history' in refresh_frames:
+                if ( parent.frames && parent.frames.galaxy_history ) {
+                    parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}";
+                    if ( parent.force_right_panel ) {
+                        parent.force_right_panel( 'show' );
+                    }
+                }
+            %endif
+            %if 'tools' in refresh_frames:
+                if ( parent.frames && parent.frames.galaxy_tools ) {
+                    parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}";
+                    if ( parent.force_left_panel ) {
+                        parent.force_left_panel( 'show' );
+                    }
+                }
+            %endif
+        %endif
+    </script>
+</%def>
+
+<%def name="stylesheets()">
+    <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
+    <style>
+        ## Not generic to all grids -- move to base?
+        .count-box {
+            min-width: 1.1em;
+            padding: 5px;
+            border-width: 1px;
+            border-style: solid;
+            text-align: center;
+            display: inline-block;
+        }
+    </style>
+</%def>
+
+<div class="grid-header">
+    <h2>Samples associated with request: ${grid.request.name}</h2>
+    <h3>User: ${grid.user.email}</h3>
+##    %if len(query.all()):
+##        <span class="title">Filter:</span>
+##        %for i, filter in enumerate( grid.standard_filters ):
+##            %if i > 0:    
+##                <span>|</span>
+##            %endif
+##            <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span>
+##        %endfor
+##    %endif
+</div>
+
+%if not len(query.all()):
+    There are no sample(s).
+%else:
+<form name="history_actions" action="${url()}" method="post" >
+    <table class="grid">
+        <thead>
+            <tr>
+                <th></th>
+                %for column in grid.columns:
+                    %if column.visible:
+                        <%
+                            href = ""
+                            extra = ""
+                            if column.sortable:
+                                if sort_key == column.key:
+                                    if sort_order == "asc":
+                                        href = url( sort=( "-" + column.key ) )
+                                        extra = "&darr;"
+                                    else:
+                                        href = url( sort=( column.key ) )
+                                        extra = "&uarr;"
+                                else:
+                                    href = url( sort=column.key )
+                        %>
+                        <th\
+                        %if column.ncells > 1:
+                            colspan="${column.ncells}"
+                        %endif
+                        >
+                            %if href:
+                                <a href="${href}">${column.label}</a>
+                            %else:
+                                ${column.label}
+                            %endif
+                            <span>${extra}</span>
+                        </th>
+                    %endif
+                %endfor
+                <th></th>
+            </tr>
+        </thead>
+        <tbody>
+            %for i, item in enumerate( query ):
+                <tr \
+                %if current_item == item:
+                    class="current" \
+                %endif
+                > 
+                    ## Item selection column
+                    <td style="width: 1.5em;">
+                        <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" />
+                    </td>
+                    ## Data columns
+                    %for column in grid.columns:
+                        %if column.visible:
+                            <%
+                                # Link
+                                if column.link and column.link( item ):
+                                    href = url( **column.link( item ) )
+                                else:
+                                    href = None
+                                # Value (coerced to list so we can loop)
+                                value = column.get_value( trans, grid, item )
+                                if column.ncells == 1:
+                                    value = [ value ]
+                            %>
+                            %for cellnum, v in enumerate( value ):
+                                <%
+                                    # Attach popup menu?
+                                    if column.attach_popup and cellnum == 0:
+                                        extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">&#9660;</a>' % i
+                                    else:
+                                        extra = ""
+                                %>
+                                %if href:                    
+                                    <td><a href="${href}">${v}</a>&nbsp;${extra}</td>
+                                %else:
+                                    <td >${v}${extra}</td>
+                                %endif    
+                                </td>
+                            %endfor
+                        %endif
+                    %endfor
+                    ## Actions column
+                    <td>
+                        <div popupmenu="grid-${i}-popup">
+                            %for operation in grid.operations:
+                                %if operation.allowed( item ):
+                                    <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a>
+                                %endif
+                            %endfor
+                        </div>
+                    </td>
+                </tr>
+            %endfor
+        </tbody>
+        <tfoot>
+            <tr>
+                <td></td>
+                <td colspan="100">
+                    For <span class="grid-selected-count"></span> selected requests:
+                    %for operation in grid.operations:
+                        %if operation.allow_multiple:
+                            <input type="submit" name="operation" value="${operation.label}" class="action-button">
+                        %endif
+                    %endfor
+                </td>
+            </tr>
+        </tfoot>
+    </table>
+</form>
+
+%endif
@@ -0,0 +1,19 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Sample Details: '${sample_details[0]['value']}'</div>
+        %for index, rd in enumerate(sample_details):
+            <div class="form-row">
+                <label>${rd['label']}</label>            
+                ${rd['value']}
+            </div>
+            <div style="clear: both"></div>
+        %endfor
+    </div>
+</div>
@@ -29,4 +29,33 @@ ${self.javascripts()}
  ## <![endif]-->
  <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script>
  <script type="text/javascript" src="${h.url_for('/static/scripts/galaxy.base.js')}"></script>
+
+
 </%def>
+
+<script type="text/javascript">
+$( function() {
+    $( "select[refresh_on_change='true']").change( function() {
+        var refresh = false;
+        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+        if ( refresh_on_change_values ) {
+            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+            for( i= 0; i < refresh_on_change_values.length; i++ ) {
+                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+                    refresh = true;
+                    break;
+                }
+            }
+        }
+        else {
+            refresh = true;
+        }
+        if ( refresh ){
+            $( ':file' ).each( function() {
+                var file_value = $( this )[0].value;
+            } );
+            $( "#edit_form" ).submit();
+        }
+    });
+});
@@ -153,6 +153,8 @@
    ${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))}

    ${tab( "libraries", "Libraries", h.url_for( controller='library', action='index' ))}
+        
+    ${tab( "requests", "Requests", h.url_for( controller='requests', action='index' ), visible = (trans.user and trans.request_types)) }

    %if app.config.get_bool( 'enable_tracks', False ):
    <span class="tab">
@@ -0,0 +1,210 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Browse Samples</%def>
+
+%if message:
+    <p>
+        <div class="${message_type}message transient-message">${message}</div>
+        <div style="clear: both"></div>
+    </p>
+%endif
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    <script type="text/javascript">        
+        ## TODO: generalize and move into galaxy.base.js
+        $(document).ready(function() {
+            $(".grid").each( function() {
+                var grid = this;
+                var checkboxes = $(this).find("input.grid-row-select-checkbox");
+                var update = $(this).find( "span.grid-selected-count" );
+                $(checkboxes).each( function() {
+                    $(this).change( function() {
+                        var n = $(checkboxes).filter("[checked]").size();
+                        update.text( n );
+                    });
+                })
+            });
+        });
+        ## Can this be moved into base.mako?
+        %if refresh_frames:
+            %if 'masthead' in refresh_frames:            
+                ## Refresh masthead == user changes (backward compatibility)
+                if ( parent.user_changed ) {
+                    %if trans.user:
+                        parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} );
+                    %else:
+                        parent.user_changed( null, false );
+                    %endif
+                }
+            %endif
+            %if 'history' in refresh_frames:
+                if ( parent.frames && parent.frames.galaxy_history ) {
+                    parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}";
+                    if ( parent.force_right_panel ) {
+                        parent.force_right_panel( 'show' );
+                    }
+                }
+            %endif
+            %if 'tools' in refresh_frames:
+                if ( parent.frames && parent.frames.galaxy_tools ) {
+                    parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}";
+                    if ( parent.force_left_panel ) {
+                        parent.force_left_panel( 'show' );
+                    }
+                }
+            %endif
+        %endif
+    </script>
+</%def>
+
+<%def name="stylesheets()">
+    <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
+    <style>
+        ## Not generic to all grids -- move to base?
+        .count-box {
+            min-width: 1.1em;
+            padding: 5px;
+            border-width: 1px;
+            border-style: solid;
+            text-align: center;
+            display: inline-block;
+        }
+    </style>
+</%def>
+
+<div class="grid-header">
+    <h2>${grid.title}</h2>
+##    %if len(query.all()):
+##        <span class="title">Filter:</span>
+##        %for i, filter in enumerate( grid.standard_filters ):
+##            %if i > 0:    
+##                <span>|</span>
+##            %endif
+##            <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span>
+##        %endfor
+##    %endif
+</div>
+
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button" href="${h.url_for( controller='requests', action='new', select_request_type=True )}">
+        <img src="${h.url_for('/static/images/silk/add.png')}" />
+        <span>New request</span></a>
+    </li>
+</ul>
+
+
+%if not len(query.all()):
+    There are no request(s).
+%else:
+<form name="history_actions" action="${url()}" method="post" >
+    <table class="grid">
+        <thead>
+            <tr>
+                <th></th>
+                %for column in grid.columns:
+                    %if column.visible:
+                        <%
+                            href = ""
+                            extra = ""
+                            if column.sortable:
+                                if sort_key == column.key:
+                                    if sort_order == "asc":
+                                        href = url( sort=( "-" + column.key ) )
+                                        extra = "&darr;"
+                                    else:
+                                        href = url( sort=( column.key ) )
+                                        extra = "&uarr;"
+                                else:
+                                    href = url( sort=column.key )
+                        %>
+                        <th\
+                        %if column.ncells > 1:
+                            colspan="${column.ncells}"
+                        %endif
+                        >
+                            %if href:
+                                <a href="${href}">${column.label}</a>
+                            %else:
+                                ${column.label}
+                            %endif
+                            <span>${extra}</span>
+                        </th>
+                    %endif
+                %endfor
+                <th></th>
+            </tr>
+        </thead>
+        <tbody>
+            %for i, item in enumerate( query ):
+                <tr \
+                %if current_item == item:
+                    class="current" \
+                %endif
+                > 
+                    ## Item selection column
+                    <td style="width: 1.5em;">
+                        <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" />
+                    </td>
+                    ## Data columns
+                    %for column in grid.columns:
+                        %if column.visible:
+                            <%
+                                # Link
+                                if column.link and column.link( item ):
+                                    href = url( **column.link( item ) )
+                                else:
+                                    href = None
+                                # Value (coerced to list so we can loop)
+                                value = column.get_value( trans, grid, item )
+                                if column.ncells == 1:
+                                    value = [ value ]
+                            %>
+                            %for cellnum, v in enumerate( value ):
+                                <%
+                                    # Attach popup menu?
+                                    if column.attach_popup and cellnum == 0:
+                                        extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">&#9660;</a>' % i
+                                    else:
+                                        extra = ""
+                                %>
+                                %if href:                    
+                                    <td><a href="${href}">${v}</a>&nbsp;${extra}</td>
+                                %else:
+                                    <td >${v}${extra}</td>
+                                %endif    
+                                </td>
+                            %endfor
+                        %endif
+                    %endfor
+                    ## Actions column
+                    <td>
+                        <div popupmenu="grid-${i}-popup">
+                            %for operation in grid.operations:
+                                %if operation.allowed( item ):
+                                    <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a>
+                                %endif
+                            %endfor
+                        </div>
+                    </td>
+                </tr>
+            %endfor
+        </tbody>
+##        <tfoot>
+##            <tr>
+##                <td></td>
+##                <td colspan="100">
+##                    For <span class="grid-selected-count"></span> selected requests:
+##                    %for operation in grid.operations:
+##                        %if operation.allow_multiple:
+##                            <input type="submit" name="operation" value="${operation.label}" class="action-button">
+##                        %endif
+##                    %endfor
+##                </td>
+##            </tr>
+##        </tfoot>
+    </table>
+</form>
+%endif
@@ -0,0 +1,16 @@
+<%inherit file="/base_panels.mako"/>
+
+<%def name="init()">
+<%
+    self.has_left_panel=False
+    self.has_right_panel=False
+    self.active_view="requests"
+    self.message_box_visible=False
+%>
+</%def>
+
+<%def name="center_panel()">
+
+    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="requests", action="list" )}"> </iframe>
+
+</%def>
@@ -0,0 +1,32 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">${title}</div>
+    <div class="toolFormBody">
+        <form name="sample" action="${h.url_for( controller='requests', action='new', save=True, request_form_id=request_form_id, request_type_id=request_type.id )}" method="post" >
+            %for i, field in enumerate(widgets):
+                <div class="form-row">
+                    <label>${field['label']}</label>
+                    ${field['widget'].get_html()}
+                    <div class="toolParamHelp" style="clear: both;">
+                        ${field['helptext']}
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+            %endfor                    
+            <div class="form-row">
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="hidden" name="new" value="submitted" size="40"/>
+                </div>
+              <div style="clear: both"></div>
+            </div>
+            <input type="submit" name="create_library_button" value="Save"/>
+        </form>
+    </div>
+</div>
@@ -0,0 +1,31 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+
+<div class="toolForm">
+    <div class="toolFormTitle">Add a new request</div>
+    %if not request_types:
+        There are no request types created for a new request.
+    %else:
+        <div class="toolFormBody">
+            <form name="select_request_type" action="${h.url_for( controller='requests', action='new', create=True )}" method="post" >
+                <div class="form-row">
+                    <label>
+                        Select Request Type:
+                    </label>
+                    <select name="request_type_id">
+                        %for rt in request_types:
+                            <option value="${rt.id}">${rt.name}</option>
+                        %endfor
+                    </select>
+                    <input type="submit" name="create_request" value="Go"/>
+                </div>
+            </form>
+        </div>
+    %endif
+</div>
@@ -0,0 +1,20 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Request Details: '${request_details[0]['value']}'</div>
+        %for index, rd in enumerate(request_details):
+            <div class="form-row">
+                <label>${rd['label']}</label>
+                ##<i>${rd['helptext']}</i>                                   
+                ${rd['value']}
+            </div>
+            <div style="clear: both"></div>
+        %endfor
+    </div>
+</div>
@@ -0,0 +1,43 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Browse Samples</%def>
+
+<h2>Samples</h2>
+
+<ul class="manage-table-actions">
+    %if not deleted:
+        <li>
+            <a class="action-button" href="${h.url_for( controller='sample', action='do', new=True )}"><span>Add Sample</span></a>
+        </li>
+    %endif
+</ul>
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+%if not samples_list:
+    You have no samples.
+%else:
+    <table class="grid">
+        <thead>
+            <tr>
+                <th>Name</th>
+                <th>Description</th>
+                <th>Type</th>
+                <th>State</th>
+            </tr>
+        </thead>
+        <tbody>
+            %for id, name, desc, st, state in samples_list:    
+                <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
+                    <td><b><a href="${h.url_for( controller='sample', action='do', sample_id=id, edit=True)}">${name}</a></b></td>
+                    <td><a>${desc}</a></td>
+                    <td><a>${st}</a></td>
+                    <td><a href="${h.url_for( controller='sample', action='events', sample_id=id)}">${state}</a></td>
+                </tr>             
+            %endfor
+        </tbody>
+    </table>
+%endif
@@ -0,0 +1,64 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Edit sample named: ${values.content['Name']}</div>
+    <div class="toolFormBody">
+        <form name="sample" action="${h.url_for( controller='sample', action='do', save_changes=True, sample_id=sample.id )}" method="post" >
+            <div class="form-row">
+                <label>
+                    Library:
+                </label>
+                <select name="library_id">
+                    %for library in libraries:
+                        <option value="${library.id}">${library.name}</option>
+                    %endfor
+                </select>
+            </div>
+            %for i, field in enumerate(form.fields):
+                <div class="form-row">
+                    <label>${field['label']}</label>
+                    %if field['type'] == 'TextField':
+                        <input type="text" name="${field['label']}" value="${values.content[field['label']]}" size="40"/>
+                    %elif field['type'] == 'TextArea':
+                        <textarea name="${field['label']}" rows="3" cols="35">${values.content[field['label']]}</textarea>
+                    %elif field['type'] == 'CheckBox':
+                        %if values.content[field['label']] == "true":
+                            <input type="checkbox" name="${field['label']}" value="true" checked>
+                        %else:
+                            <input type="checkbox" name="${field['label']}" value="true">
+                        %endif
+                    %elif field['type'] == 'SelectBox':
+                        <select name="${field['label']}">
+                            %for ft in field['selectlist']:
+                                %if ft == values.content[field['label']]:
+                                    <option value="${ft}" selected>${ft}</option>
+                                %else:
+                                    <option value="${ft}">${ft}</option>
+                                %endif
+                            %endfor
+                        </select>
+                    %endif
+                    <div class="toolParamHelp" style="clear: both;">
+                    ${field['helptext']}
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+            %endfor                    
+            <div class="form-row">
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="hidden" name="new" value="submitted" size="40"/>
+                </div>
+              <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <input type="submit" name="create_library_button" value="Save"/>
+            </div>
+        </form>
+    </div>
+</div>
@@ -0,0 +1,210 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Browse Samples</%def>
+
+%if message:
+    <p>
+        <div class="${message_type}message transient-message">${message}</div>
+        <div style="clear: both"></div>
+    </p>
+%endif
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    <script type="text/javascript">        
+        ## TODO: generalize and move into galaxy.base.js
+        $(document).ready(function() {
+            $(".grid").each( function() {
+                var grid = this;
+                var checkboxes = $(this).find("input.grid-row-select-checkbox");
+                var update = $(this).find( "span.grid-selected-count" );
+                $(checkboxes).each( function() {
+                    $(this).change( function() {
+                        var n = $(checkboxes).filter("[checked]").size();
+                        update.text( n );
+                    });
+                })
+            });
+        });
+        ## Can this be moved into base.mako?
+        %if refresh_frames:
+            %if 'masthead' in refresh_frames:            
+                ## Refresh masthead == user changes (backward compatibility)
+                if ( parent.user_changed ) {
+                    %if trans.user:
+                        parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} );
+                    %else:
+                        parent.user_changed( null, false );
+                    %endif
+                }
+            %endif
+            %if 'history' in refresh_frames:
+                if ( parent.frames && parent.frames.galaxy_history ) {
+                    parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}";
+                    if ( parent.force_right_panel ) {
+                        parent.force_right_panel( 'show' );
+                    }
+                }
+            %endif
+            %if 'tools' in refresh_frames:
+                if ( parent.frames && parent.frames.galaxy_tools ) {
+                    parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}";
+                    if ( parent.force_left_panel ) {
+                        parent.force_left_panel( 'show' );
+                    }
+                }
+            %endif
+        %endif
+    </script>
+</%def>
+
+<%def name="stylesheets()">
+    <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
+    <style>
+        ## Not generic to all grids -- move to base?
+        .count-box {
+            min-width: 1.1em;
+            padding: 5px;
+            border-width: 1px;
+            border-style: solid;
+            text-align: center;
+            display: inline-block;
+        }
+    </style>
+</%def>
+
+<div class="grid-header">
+    <h2>Samples associated with request: ${grid.request.name}</h2>
+##    %if len(query.all()):
+##        <span class="title">Filter:</span>
+##        %for i, filter in enumerate( grid.standard_filters ):
+##            %if i > 0:    
+##                <span>|</span>
+##            %endif
+##            <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span>
+##        %endfor
+##    %endif
+</div>
+
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button" href="${h.url_for( controller='requests', action='add_sample', id=grid.request.id)}">
+        <img src="${h.url_for('/static/images/silk/add.png')}" />
+        <span>Add sample</span></a>
+    </li>
+</ul>
+
+%if not len(query.all()):
+    There are no sample(s).
+%else:
+<form name="history_actions" action="${url()}" method="post" >
+    <table class="grid">
+        <thead>
+            <tr>
+                <th></th>
+                %for column in grid.columns:
+                    %if column.visible:
+                        <%
+                            href = ""
+                            extra = ""
+                            if column.sortable:
+                                if sort_key == column.key:
+                                    if sort_order == "asc":
+                                        href = url( sort=( "-" + column.key ) )
+                                        extra = "&darr;"
+                                    else:
+                                        href = url( sort=( column.key ) )
+                                        extra = "&uarr;"
+                                else:
+                                    href = url( sort=column.key )
+                        %>
+                        <th\
+                        %if column.ncells > 1:
+                            colspan="${column.ncells}"
+                        %endif
+                        >
+                            %if href:
+                                <a href="${href}">${column.label}</a>
+                            %else:
+                                ${column.label}
+                            %endif
+                            <span>${extra}</span>
+                        </th>
+                    %endif
+                %endfor
+                <th></th>
+            </tr>
+        </thead>
+        <tbody>
+            %for i, item in enumerate( query ):
+                <tr \
+                %if current_item == item:
+                    class="current" \
+                %endif
+                > 
+                    ## Item selection column
+                    <td style="width: 1.5em;">
+                        <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" />
+                    </td>
+                    ## Data columns
+                    %for column in grid.columns:
+                        %if column.visible:
+                            <%
+                                # Link
+                                if column.link and column.link( item ):
+                                    href = url( **column.link( item ) )
+                                else:
+                                    href = None
+                                # Value (coerced to list so we can loop)
+                                value = column.get_value( trans, grid, item )
+                                if column.ncells == 1:
+                                    value = [ value ]
+                            %>
+                            %for cellnum, v in enumerate( value ):
+                                <%
+                                    # Attach popup menu?
+                                    if column.attach_popup and cellnum == 0:
+                                        extra = '<a id="grid-%d-popup" class="popup-arrow" style="display: none;">&#9660;</a>' % i
+                                    else:
+                                        extra = ""
+                                %>
+                                %if href:                    
+                                    <td><a href="${href}">${v}</a>&nbsp;${extra}</td>
+                                %else:
+                                    <td >${v}${extra}</td>
+                                %endif    
+                                </td>
+                            %endfor
+                        %endif
+                    %endfor
+                    ## Actions column
+##                    <td>
+##                        <div popupmenu="grid-${i}-popup">
+##                            %for operation in grid.operations:
+##                                %if operation.allowed( item ):
+##                                    <a class="action-button" href="${url( operation=operation.label, id=trans.security.encode_id( item.id ) )}">${operation.label}</a>
+##                                %endif
+##                            %endfor
+##                        </div>
+##                    </td>
+                </tr>
+            %endfor
+        </tbody>
+##        <tfoot>
+##            <tr>
+##                <td></td>
+##                <td colspan="100">
+##                    For <span class="grid-selected-count"></span> selected requests:
+##                    %for operation in grid.operations:
+##                        %if operation.allow_multiple:
+##                            <input type="submit" name="operation" value="${operation.label}" class="action-button">
+##                        %endif
+##                    %endfor
+##                </td>
+##            </tr>
+##        </tfoot>
+    </table>
+</form>
+
+%endif
@@ -0,0 +1,16 @@
+<%inherit file="/base_panels.mako"/>
+
+<%def name="init()">
+<%
+    self.has_left_panel=False
+    self.has_right_panel=False
+    self.active_view="requests"
+
+%>
+</%def>
+
+<%def name="center_panel()">
+
+    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="sample", action="list", request_id=request_id )}"> </iframe>
+
+</%def>
@@ -0,0 +1,32 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">${title}</div>
+    <div class="toolFormBody">
+        <form name="sample" action="${h.url_for( controller='requests', action='samples', save=True, sample_form_id=sample_form_id, request_id=request_id )}" method="post" >
+            %for i, field in enumerate(widgets):
+                <div class="form-row">
+                    <label>${field['label']}</label>
+                    ${field['widget'].get_html()}
+                    <div class="toolParamHelp" style="clear: both;">
+                        ${field['helptext']}
+                    </div>
+                    <div style="clear: both"></div>
+                </div>
+            %endfor                    
+            <div class="form-row">
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="hidden" name="new" value="submitted" size="40"/>
+                </div>
+              <div style="clear: both"></div>
+            </div>
+            <input type="submit" name="create_sample_button" value="Save"/>
+        </form>
+    </div>
+</div>
@@ -0,0 +1,32 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+<%def name="title()">Events for Sample ${sample_name}</%def>
+
+<h2>Events for Sample "${sample_name}" of Request: ${request}</h2>
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+
+<table class="grid">
+    <thead>
+        <tr>
+            <th>State</th>
+            <th>Updated</th>
+            <th>Description</th>
+            <th>Comments</th>
+        </tr>
+    </thead>
+    <tbody>
+        %for state, updated, desc, comments in events_list:    
+            <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
+                <td><b><a>${state}</a></b></td>
+                <td><a>${updated}</a></td>
+                <td><a>${desc}</a></td>
+                <td><a>${comments}</a></td>
+            </tr>             
+        %endfor
+    </tbody>
+</table>
@@ -0,0 +1,19 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Sample Details: '${sample_details[0]['value']}'</div>
+       %for index, rd in enumerate(sample_details):
+            <div class="form-row">
+                <label>${rd['label']}</label>            
+                ${rd['value']}
+            </div>
+            <div style="clear: both"></div>
+       %endfor
+    </div>
+</div>