[galaxy-dev] [hg] galaxy 2882: Forms & request controllers

14 Oct 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/ca816e66ec69
changeset: 2882:ca816e66ec69
user:      rc
date:      Wed Oct 14 02:22:11 2009 -0400
description:
Forms & request controllers
    - refactored to work on main
    - cleanup
Added more functional tests
12 file(s) affected in this change:
lib/galaxy/model/__init__.py
lib/galaxy/web/controllers/forms.py
lib/galaxy/web/controllers/requests.py
lib/galaxy/web/controllers/requests_admin.py
lib/galaxy/web/framework/__init__.py
templates/admin/forms/edit_form.mako
templates/admin/forms/show_form_read_only.mako
templates/admin/requests/show_request.mako
templates/requests/show_request.mako
templates/user/address.mako
test/base/twilltestcase.py
test/functional/test_forms_and_requests.py
diffs (2308 lines):
diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py	Tue Oct 13 18:15:06 2009 -0400
+++ b/lib/galaxy/model/__init__.py	Wed Oct 14 02:22:11 2009 -0400
@@ -1090,11 +1090,12 @@
     types = Bunch(  REQUEST = 'Sequencing Request Form',
                     SAMPLE = 'Sequencing Sample Form',
                     LIBRARY_INFO_TEMPLATE = 'Library information template'  )
-    def __init__(self, name=None, desc=None, fields=[], current_form=None, form_type=None, layout=None):
+    def __init__(self, name=None, desc=None, fields=[], 
+                 form_definition_current=None, form_type=None, layout=None):
         self.name = name
         self.desc = desc
         self.fields = fields 
-        self.form_definition_current = current_form
+        self.form_definition_current = form_definition_current
         self.type = form_type
         self.layout = layout
     def fields_of_grid(self, layout_grid_name):
@@ -1263,20 +1264,26 @@
         self.postal_code = postal_code
         self.country = country
         self.phone = phone
-    def display(self):
-        return  self.name+'<br/>'+ \
-                self.institution+'<br/>'+ \
-                self.address+'<br/>'+ \
-                self.city+' '+self.state+' '+self.postal_code+'<br/>'+ \
-                self.country+'<br/>'+ \
-                'Phone: '+self.phone
     def get_html(self):
-        return  self.name+'<br/>'+ \
-                self.institution+'<br/>'+ \
-                self.address+'<br/>'+ \
-                self.city+' '+self.state+' '+self.postal_code+'<br/>'+ \
-                self.country+'<br/>'+ \
-                'Phone: '+self.phone
+        html = ''
+        if self.name:
+            html = html + self.name
+        if self.institution:
+            html = html + '<br/>' + self.institution
+        if self.address:
+            html = html + '<br/>' + self.address
+        if self.city:
+            html = html + '<br/>' + self.city
+        if self.state:
+            html = html + ' ' + self.state
+        if self.postal_code:
+            html = html + ' ' + self.postal_code
+        if self.country:
+            html = html + '<br/>' + self.country
+        if self.phone:
+            html = html + '<br/>' + 'Phone: ' + self.phone
+        return html
+
class Page( object ):
     def __init__( self ):
diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/web/controllers/forms.py
--- a/lib/galaxy/web/controllers/forms.py	Tue Oct 13 18:15:06 2009 -0400
+++ b/lib/galaxy/web/controllers/forms.py	Wed Oct 14 02:22:11 2009 -0400
@@ -12,6 +12,14 @@
 log = logging.getLogger( __name__ )
class Forms( BaseController ):
+    # Empty form field
+    empty_field = { 'label': '', 
+                    'helptext': '', 
+                    'visible': True,
+                    'required': False,
+                    'type': BaseField.form_field_types()[0],
+                    'selectlist': [],
+                    'layout': 'none' }
     @web.expose
     @web.require_admin
     def index( self, trans, **kwd ):
@@ -84,19 +92,12 @@
                                                                   action='edit',
                                                                   form_id=fd.id,
                                                                   add_field_button='Add field',
-                                                                  num_fields=0,
                                                                   name=fd.name,
                                                                   description=fd.desc,
                                                                   form_type_selectbox=fd.type ) )  
-        self.current_form = {}
-        self.current_form[ 'name' ] = 'New Form'
-        self.current_form[ 'desc' ] = ''
-        self.current_form[ 'type' ] = params.get( 'form_type', 'none' )
-        self.current_form[ 'layout' ] = [ 'Main' ]
-        self.current_form[ 'fields' ] = []
-        inputs = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ),
-                   ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ),
-                   ( 'Type', self.__form_types_widget(trans, selected=self.current_form['type']) ),
+        inputs = [ ( 'Name', TextField( 'name', 40, 'New Form' ) ),
+                   ( 'Description', TextField( 'description', 40, '' ) ),
+                   ( 'Type', self.__form_types_widget(trans, selected=params.get( 'form_type', 'none' )) ),
                    ( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ]
         return trans.fill_template( '/admin/forms/create_form.mako', 
                                     inputs=inputs,
@@ -134,102 +135,156 @@
         renaming fields, adding/deleting fields, changing fields attributes.
         '''
         params = util.Params( kwd )
+        log.debug( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        form_id = params.get( 'form_id', None )
-        if not form_id:
-            msg = 'Invalid form id %s' % str( form_id )
-            trans.response.send_redirect( web.url_for( controller='forms',
-                                                       action='manage',
-                                                       msg=msg,
-                                                       messagetype='error' ) )
-        fd = trans.app.model.FormDefinition.get( int( params.form_id ) )
+        try:
+            fd = trans.app.model.FormDefinition.get( int( params.get( 'form_id', None ) ) )
+        except:
+            return trans.response.send_redirect( web.url_for( controller='forms',
+                                                              action='manage',
+                                                              msg='Invalid form',
+                                                              messagetype='error' ) )
+        #
         # Show the form for editing
+        #
         if params.get( 'show_form', False ):
-            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=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
-        #Add a layout grid
+            current_form = self.__get_saved_form( fd )
+            return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                msg=msg, messagetype=messagetype, **kwd )
+        #
+        # Add a layout grid
+        #
         elif params.get( 'add_layout_grid', False ):
-            self.__update_current_form( trans, **kwd )
-            self.__add_layout_grid()
+            current_form = self.__get_form( trans, **kwd )
+            current_form['layout'].append('')
             # show the form again
-            return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
+            return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                msg=msg, messagetype=messagetype, **kwd )
+        #
         # Delete a layout grid
+        #
         elif params.get( 'remove_layout_grid_button', False ):
-            self.__update_current_form( trans, **kwd )
+            current_form = self.__get_form( trans, **kwd )
             index = int( kwd[ 'remove_layout_grid_button' ].split( ' ' )[2] ) - 1
-            self.__remove_layout_grid( index )
-            return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )   
+            del current_form['layout'][index]
+            return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                msg=msg, messagetype=messagetype, **kwd )
+        #
+        # Add a field
+        #
+        elif params.get( 'add_field_button', False ):
+            current_form = self.__get_form( trans, **kwd )
+            current_form['fields'].append( self.empty_field )
+            # show the form again with one empty field
+            return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                msg=msg, messagetype=messagetype, **kwd )
+        #
         # Delete a field
+        #
         elif params.get( 'remove_button', False ):
-            self.__update_current_form( trans, **kwd )
+            current_form = self.__get_form( trans, **kwd )
+            # find the index of the field to be removed from the remove button label
             index = int( kwd[ 'remove_button' ].split( ' ' )[2] ) - 1
-            self.__remove_field( index )
-            return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )          
+            del current_form['fields'][index]
+            return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                msg=msg, messagetype=messagetype, **kwd )
+        #
         # Save changes
+        #
         elif params.get( 'save_changes_button', False ):
-            self.__update_current_form( trans, **kwd )
-            fd_new, msg = self.__save_form( trans, fd.form_definition_current.id, **kwd )
+            fd_new, msg = self.__save_form( trans, fdc_id=fd.form_definition_current.id, **kwd )
+            # if validation error encountered while saving the form, show the 
+            # unsaved form, with the error message
             if not fd_new:
-                return self.__show( trans=trans, form=fd, msg=msg, messagetype='error', **kwd )
-            else:
-                fd = fd_new
+                current_form = self.__get_form( trans, **kwd )
+                return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                    msg=msg, messagetype='error', **kwd )
+            # everything went fine. form saved successfully. Show the saved form
+            fd = fd_new
+            current_form = self.__get_saved_form( fd )
             msg = "The form '%s' has been updated with the changes." % fd.name
-            return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
-        #Add a field
-        elif params.get( 'add_field_button', False ):
-            self.__update_current_form( trans, **kwd )
-            self.__add_field()
-            # show the form again with one empty field
-            return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
+            return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                msg=msg, messagetype=messagetype, **kwd )
+        #
         # 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
+        #
+        # Add SelectField option
+        #
+        elif 'Add' in kwd.values():
+            return self.__add_selectbox_option(trans, fd, msg, messagetype, **kwd)
+        #
+        # Remove SelectField option
+        #
+        elif 'Remove' in kwd.values():
+            return self.__remove_selectbox_option(trans, fd, msg, messagetype, **kwd)
+        #
+        # Refresh page
+        #
         elif params.get( 'refresh', False ):
-            self.__update_current_form( trans, **kwd )
-            return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
-        # Remove SelectField option
-        elif params.get( 'select_box_options', False ) == 'remove':
-            index = int( kwd[ 'field_index' ] )
-            option = int( kwd[ 'option_index' ] )
-            del self.current_form[ 'fields' ][ index ][ 'selectlist' ][ option ]
-            return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
-        # Add SelectField option
-        elif params.get( 'select_box_options', False ) == 'add':
-            index = int( kwd[ 'field_index' ] )
-            self.current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' )
-            return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )   
-    def __add_layout_grid(self):
-        self.current_form['layout'].append('')
-    def __remove_layout_grid(self, index):
-        del self.current_form['layout'][index]
-    def __remove_field(self, index):
-        del self.current_form['fields'][index]
-    def __add_field(self):
+            current_form = self.__get_form( trans, **kwd )
+            return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                msg=msg, messagetype=messagetype, **kwd )
+            
+    def __add_selectbox_option( self, trans, fd, msg, messagetype, **kwd ):
         '''
-        add an empty field to the fields list
+        This method adds a selectbox option. The kwd dict searched for
+        the field index which needs to be removed
         '''
-        empty_field = { 'label': '', 
-                        'helptext': '', 
-                        'visible': True,
-                        'required': False,
-                        'type': BaseField.form_field_types()[0],
-                        'selectlist': [],
-                        'layout': 'none' }
-        self.current_form['fields'].append(empty_field)
+        current_form = self.__get_form( trans, **kwd )
+        index = -1
+        for k, v in kwd.items():
+            if v == 'Add':
+                # extract the field index from the
+                # button name of format: 'addoption_<field>'
+                index = int(k.split('_')[1])
+                break
+        if index == -1:
+            # something wrong happened
+            return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                msg='Error in adding selectfield option', 
+                                messagetype='error', **kwd )
+        # add an empty option
+        current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' )
+        return self.__show( trans=trans, form=fd, current_form=current_form, 
+                            msg=msg, messagetype=messagetype, **kwd )
+    def __remove_selectbox_option( self, trans, fd, msg, messagetype, **kwd ):
+        '''
+        This method removes a selectbox option. The kwd dict searched for
+        the field index and option index which needs to be removed
+        '''
+        current_form = self.__get_form( trans, **kwd )
+        option = -1
+        for k, v in kwd.items():
+            if v == 'Remove':
+                # extract the field & option indices from the
+                # button name of format: 'removeoption_<field>_<option>'
+                index = int(k.split('_')[1])
+                option = int(k.split('_')[2])
+                break
+        if option == -1:
+            # something wrong happened
+            return self.__show( trans=trans, form=fd, current_form=current_form, 
+                                msg='Error in removing selectfield option', 
+                                messagetype='error', **kwd )
+        # remove the option
+        del current_form[ 'fields' ][ index ][ 'selectlist' ][ option ]
+        return self.__show( trans=trans, form=fd, current_form=current_form, 
+                            msg=msg, messagetype=messagetype, **kwd )
+
+    
     def __get_field(self, index, **kwd):
+        '''
+        This method retrieves all the user-entered details of a field and
+        returns a dict.
+        '''
         params = util.Params( kwd )
-        #TODO: RC this needs to be handled so that it does not throw an exception.
-        # To reproduce, create a new form, click the "add field" button, click the
-        # browser back arrow, then click the "add field" button again.
-        # You should never attempt to "restore_text()" on a None object...
         name = util.restore_text( params.get( 'field_name_%i' % index, '' ) )
         helptext = util.restore_text( params.get( 'field_helptext_%i' % index, '' ) )
         required =  params.get( 'field_required_%i' % index, False )
@@ -266,57 +321,54 @@
             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['type'] = fd.type
-        self.current_form['layout'] = list(copy.deepcopy(fd.layout))
-        self.current_form['fields'] = list(copy.deepcopy(fd.fields))
-    def __validate_form(self, **kwd):
         '''
-        This method checks the following text inputs are filled out by the user
-        - the name of form
-        - name of all the fields
+        This retrieves the saved form and returns a dictionary containing the name, 
+        desc, type, layout & fields of the form
         '''
-        params = util.Params( kwd )
-        # form name
-        if not util.restore_text( params.name ):
-            return None, 'Form name must be filled.'
-        # form type
-        if util.restore_text( params.form_type_selectbox ) == 'none': 
-            return None, 'Form type must be selected.'        
-        # fields
-#        for i in range( len(self.current_form['fields']) ):
-#            if not util.restore_text(params.get( 'field_name_%i' % i, None )):
-#                return None, "All the field label(s) must be completed."
-        return True, ''
+        return dict(name = fd.name,
+                    desc = fd.desc,
+                    type = fd.type,
+                    layout = list(copy.deepcopy(fd.layout)),
+                    fields = list(copy.deepcopy(fd.fields)))
     def __get_form(self, trans, **kwd):
+        '''
+        This method gets all the user-entered form details and returns a 
+        dictionary containing the name, desc, type, layout & fields of the form
+        '''
         params = util.Params( kwd )
         name = util.restore_text( params.name ) 
         desc = util.restore_text( params.description ) or ""
         form_type = util.restore_text( params.form_type_selectbox )
+        # get the user entered layout grids 
         layout = []
-        if form_type == trans.app.model.FormDefinition.types.SAMPLE:
-            for index in range(len(self.current_form[ 'layout' ])):
-                layout.append(params.get( 'grid_layout%i' % index, '' ))
+        index = 0
+        while True:
+            grid_name = util.restore_text( params.get( 'grid_layout%i' % index, '' ) )
+            if grid_name:
+                layout.append( grid_name )
+                index = index + 1
+            else:
+                break
+        # for csv file import
         csv_file = params.get( 'file_data', '' )
+        fields = []
         if csv_file == '':
-            # set form fields
-            fields = []
-            for i in range( len(self.current_form['fields']) ):
-                fields.append(self.__get_field(i, **kwd))
+            # get the user entered fields
+            index = 0
+            while True:
+                if params.get( 'field_name_%i' % index, False ):
+                    fields.append( self.__get_field( index, **kwd ) )
+                    index = index + 1
+                else:
+                    break
             fields = fields
         else:
             fields, layout = self.__import_fields(trans, csv_file, form_type)
-        return name, desc, form_type, layout, fields
-    def __update_current_form(self, trans, **kwd):
-        name, desc, form_type, layout, fields = self.__get_form(trans, **kwd)
-        self.current_form = {}
-        self.current_form['name'] = name
-        self.current_form['desc'] = desc
-        self.current_form['type'] = form_type
-        self.current_form['layout'] = layout
-        self.current_form['fields'] = fields
+        return dict(name = name,
+                    desc = desc,
+                    type = form_type,
+                    layout = layout,
+                    fields = fields)
def __import_fields(self, trans, csv_file, form_type):
         '''
@@ -356,7 +408,20 @@
                                                               **kwd))
         self.__imported_from_file = True
         return fields, list(layouts)
-
+    def __validate_form(self, **kwd):
+        '''
+        This method checks the following text inputs are filled out by the user
+        - the name of form
+        - form type
+        '''
+        params = util.Params( kwd )
+        # form name
+        if not util.restore_text( params.name ):
+            return None, 'Form name must be filled.'
+        # form type
+        if util.restore_text( params.form_type_selectbox ) == 'none': 
+            return None, 'Form type must be selected.'        
+        return True, ''
     def __save_form(self, trans, fdc_id=None, **kwd):
         '''
         This method saves the current form 
@@ -365,13 +430,18 @@
         flag, msg = self.__validate_form(**kwd)
         if not flag:
             return None, msg
-        name, desc, form_type, layout, fields = self.__get_form(trans, **kwd)
+        current_form = self.__get_form( trans, **kwd )
         # validate fields
-        for field in fields:
+        for field in current_form[ 'fields' ]:
             if not field[ 'label' ]:
                 return None, "All the field label(s) must be completed."
-        fd = trans.app.model.FormDefinition(name, desc, fields, current_form=None, 
-                                            form_type=form_type, layout=layout )
+        # create a new form definition
+        fd = trans.app.model.FormDefinition(name=current_form[ 'name' ], 
+                                            desc=current_form[ 'desc' ], 
+                                            fields=current_form[ 'fields' ], 
+                                            form_definition_current=None, 
+                                            form_type=current_form[ 'type' ], 
+                                            layout=current_form[ 'layout' ] )
         if fdc_id: # save changes to the existing form    
             # change the pointer in the form_definition_current table to point 
             # to this new record
@@ -467,7 +537,7 @@
         def label(self):
             return str(self.index)+'.'+self.label
-    def __show( self, trans, form, msg='', messagetype='done', **kwd ):
+    def __show( self, trans, form, current_form, msg='', messagetype='done', **kwd ):
         '''
         This method displays the form and any of the changes made to it,
         The empty_form param allows for this method to simulate clicking
@@ -476,18 +546,18 @@
         '''
         params = util.Params( kwd )
         # name & description
-        form_details = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ),
-                         ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ),
-                         ( 'Type', self.__form_types_widget(trans, selected=self.current_form['type']) ) ]
+        form_details = [ ( 'Name', TextField( 'name', 40, current_form[ 'name' ] ) ),
+                         ( 'Description', TextField( 'description', 40, current_form[ 'desc' ] ) ),
+                         ( 'Type', self.__form_types_widget(trans, selected=current_form[ 'type' ]) ) ]
         form_layout = []
-        if self.current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE:
-            for index, lg in enumerate(self.current_form['layout']):
+        if current_form[ 'type' ] == trans.app.model.FormDefinition.types.SAMPLE:
+            for index, lg in enumerate(current_form[ 'layout' ]):
                 form_layout.append( TextField( 'grid_layout%i' % index, 40, lg )) 
         # fields
         field_details = []
-        for index, field in enumerate( self.current_form[ 'fields' ] ):
-            if self.current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE:
-                field_ui = self.FieldUI( self.current_form['layout'], index, field )
+        for index, field in enumerate( current_form[ 'fields' ] ):
+            if current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE:
+                field_ui = self.FieldUI( current_form['layout'], index, field )
             else:
                 field_ui = self.FieldUI( None, index, field )
             field_details.append( field_ui.get() )
@@ -498,7 +568,7 @@
                                     field_types=BaseField.form_field_types(),
                                     msg=msg,
                                     messagetype=messagetype,
-                                    current_form_type=self.current_form['type'],
+                                    current_form_type=current_form[ 'type' ],
                                     layout_grids=form_layout )
# Common methods for all components that use forms
diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/web/controllers/requests.py
--- a/lib/galaxy/web/controllers/requests.py	Tue Oct 13 18:15:06 2009 -0400
+++ b/lib/galaxy/web/controllers/requests.py	Wed Oct 14 02:22:11 2009 -0400
@@ -115,20 +115,17 @@
                                                               status='error',
                                                               message="Invalid request ID",
                                                               **kwd) )
-        self.current_samples = []
-        self.edit_mode = False
+        current_samples = []
         for s in request.samples:
-            self.current_samples.append([s.name, s.values.content])
+            current_samples.append([s.name, s.values.content])
         if add_sample:
-            self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]])
-        self.details_state = 'Show request details'
+            current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
         return trans.fill_template( '/requests/show_request.mako',
                                     request=request,
                                     request_details=self.request_details(trans, id),
-                                    current_samples = self.current_samples,
-                                    sample_copy=self.__copy_sample(), 
-                                    details_state=self.details_state,
-                                    edit_mode=self.edit_mode)
+                                    current_samples = current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details='hide', edit_mode='False')
     def request_details(self, trans, id):
         '''
         Shows the request details
@@ -186,25 +183,34 @@
                                             value=request.values.content[index],
                                             helptext=field['helptext']+' ('+req+')'))
         return request_details   
-    
     def __update_samples(self, request, **kwd):
+        '''
+        This method retrieves all the user entered sample information and
+        returns an list of all the samples and their field values
+        '''
         params = util.Params( kwd )
-        num_samples = len(self.current_samples)
-        self.current_samples = []
+        current_samples = []
         for s in request.samples:
-            self.current_samples.append([s.name, s.values.content])
-        for index in range(num_samples-len(request.samples)):
-            sample_index = index + len(request.samples)
-            sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-            sample_values = []
-            for field_index in range(len(request.type.sample_form.fields)):
-                sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-            self.current_samples.append([sample_name, sample_values])
-            
-    def __copy_sample(self):
+            current_samples.append([s.name, s.values.content])
+        index = len(request.samples) 
+        while True:
+            if params.get( 'sample_%i_name' % index, ''  ):
+                sample_index = index
+                sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
+                sample_values = []
+                for field_index in range(len(request.type.sample_form.fields)):
+                    sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
+                current_samples.append([sample_name, sample_values])
+                index = index + 1
+            else:
+                break
+        details = params.get( 'details', 'hide' )
+        edit_mode = params.get( 'edit_mode', 'False' )
+        return current_samples, details, edit_mode
+    def __copy_sample(self, current_samples):
         copy_list = SelectField('copy_sample')
         copy_list.add_option('None', -1, selected=True)  
-        for i, s in enumerate(self.current_samples):
+        for i, s in enumerate(current_samples):
             copy_list.add_option(s[0], i)
         return copy_list   
     @web.expose
@@ -221,20 +227,22 @@
                                                               status='error',
                                                               message="Invalid request ID",
                                                               **kwd) )
+        # get the user entered sample details
+        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
         if params.get('import_samples_button', False) == 'Import samples':
             try:
                 file_obj = params.get('file_data', '')
                 import csv
                 reader = csv.reader(file_obj.file)
                 for row in reader:
-                    self.current_samples.append([row[0], row[1:]])  
+                    current_samples.append([row[0], row[1:]])  
                 return trans.fill_template( '/requests/show_request.mako',
                                             request=request,
                                             request_details=self.request_details(trans, request.id),
-                                            current_samples=self.current_samples,
-                                            sample_copy=self.__copy_sample(), 
-                                            details_state=self.details_state,
-                                            edit_mode=self.edit_mode)
+                                            current_samples=current_samples,
+                                            sample_copy=self.__copy_sample(current_samples), 
+                                            details=details,
+                                            edit_mode=edit_mode)
             except:
                 return trans.response.send_redirect( web.url_for( controller='requests',
                                                                   action='list',
@@ -242,39 +250,35 @@
                                                                   message='Error in importing samples file',
                                                                   **kwd))
         elif params.get('add_sample_button', False) == 'Add New':
-            # save the all (saved+unsaved) sample info in 'current_samples'
-            self.__update_samples(request, **kwd)
             # add an empty or filled sample
             # if the user has selected a sample no. to copy then copy the contents 
             # of the src sample to the new sample else an empty sample
             src_sample_index = int(params.get( 'copy_sample', -1  ))
             if src_sample_index == -1:
                 # empty sample
-                self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]])
+                current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
             else:
-                self.current_samples.append([self.current_samples[src_sample_index][0]+'_%i' % (len(self.current_samples)+1),
-                                                                  [val for val in self.current_samples[src_sample_index][1]]])
+                current_samples.append([current_samples[src_sample_index][0]+'_%i' % (len(current_samples)+1),
+                                                                  [val for val in current_samples[src_sample_index][1]]])
             return trans.fill_template( '/requests/show_request.mako',
                                         request=request,
                                         request_details=self.request_details(trans, request.id),
-                                        current_samples=self.current_samples,
-                                        sample_copy=self.__copy_sample(), 
-                                        details_state=self.details_state,
-                                        edit_mode=self.edit_mode)
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details,
+                                        edit_mode=edit_mode)
         elif params.get('save_samples_button', False) == 'Save':
-            # update current_samples
-            self.__update_samples(request, **kwd)
             # check for duplicate sample names
             msg = ''
-            for index in range(len(self.current_samples)-len(request.samples)):
+            for index in range(len(current_samples)-len(request.samples)):
                 sample_index = index + len(request.samples)
-                sample_name = self.current_samples[sample_index][0]
+                sample_name = current_samples[sample_index][0]
                 if not sample_name.strip():
                     msg = 'Please enter the name of sample number %i' % sample_index
                     break
                 count = 0
-                for i in range(len(self.current_samples)):
-                    if sample_name == self.current_samples[i][0]:
+                for i in range(len(current_samples)):
+                    if sample_name == current_samples[i][0]:
                         count = count + 1
                 if count > 1: 
                     msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
@@ -283,12 +287,13 @@
                 return trans.fill_template( '/requests/show_request.mako',
                                             request=request,
                                             request_details=self.request_details(trans, request.id),
-                                            current_samples = self.current_samples,
-                                            sample_copy=self.__copy_sample(), details_state=self.details_state,
+                                            current_samples = current_samples,
+                                            sample_copy=self.__copy_sample(current_samples), 
+                                            details=details, edit_mode=edit_mode,
                                             messagetype='error', msg=msg)
             # save all the new/unsaved samples entered by the user
-            if not self.edit_mode:
-                for index in range(len(self.current_samples)-len(request.samples)):
+            if edit_mode == 'False':
+                for index in range(len(current_samples)-len(request.samples)):
                     sample_index = index + len(request.samples)
                     sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
                     sample_values = []
@@ -299,9 +304,9 @@
                     s = trans.app.model.Sample(sample_name, '', request, form_values)
                     s.flush()
             else:
-                for index in range(len(self.current_samples)):
+                for index in range(len(current_samples)):
                     sample_index = index
-                    sample_name = self.current_samples[sample_index][0]
+                    sample_name = current_samples[sample_index][0]
                     new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
                     sample_values = []
                     for field_index in range(len(request.type.sample_form.fields)):
@@ -318,14 +323,14 @@
                                                           operation='show_request',
                                                           id=trans.security.encode_id(request.id)) )
         elif params.get('edit_samples_button', False) == 'Edit samples':
-            self.edit_mode = True
+            edit_mode = 'True'
             return trans.fill_template( '/requests/show_request.mako',
                                         request=request,
                                         request_details=self.request_details(trans, request.id),
-                                        current_samples=self.current_samples,
-                                        sample_copy=self.__copy_sample(), 
-                                        details_state=self.details_state,
-                                        edit_mode=self.edit_mode)
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details,
+                                        edit_mode=edit_mode)
         elif params.get('cancel_changes_button', False) == 'Cancel':
             return trans.response.send_redirect( web.url_for( controller='requests',
                                                           action='list',
@@ -340,21 +345,22 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         request = trans.app.model.Request.get(int(params.get('request_id', 0)))
+        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
         sample_index = int(params.get('sample_id', 0))
-        sample_name = self.current_samples[sample_index][0]
+        sample_name = current_samples[sample_index][0]
         s = request.has_sample(sample_name)
         if s:
             s.delete()
             s.flush()
             request.flush()
-        del self.current_samples[sample_index]  
+        del current_samples[sample_index]  
         return trans.fill_template( '/requests/show_request.mako',
                                     request=request,
                                     request_details=self.request_details(trans, request.id),
-                                    current_samples = self.current_samples,
-                                    sample_copy=self.__copy_sample(), 
-                                    details_state=self.details_state,
-                                    edit_mode=self.edit_mode)
+                                    current_samples = current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details=details,
+                                    edit_mode=edit_mode)
@web.expose
     @web.require_login( "create/submit sequencing requests" )
@@ -363,17 +369,14 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         request = trans.app.model.Request.get(int(params.get('request_id', 0)))
-        if self.details_state == 'Show request details':
-             self.details_state = 'Hide request details'
-        elif self.details_state == 'Hide request details':
-             self.details_state = 'Show request details' 
+        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
         return trans.fill_template( '/requests/show_request.mako',
                                     request=request,
                                     request_details=self.request_details(trans, request.id),
-                                    current_samples = self.current_samples,
-                                    sample_copy=self.__copy_sample(), 
-                                    details_state=self.details_state,
-                                    edit_mode=self.edit_mode)
+                                    current_samples = current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details=details,
+                                    edit_mode=edit_mode)
     def __select_request_type(self, trans, rtid):
         rt_ids = ['none']
         for rt in trans.app.model.RequestType.query().all():
@@ -476,17 +479,22 @@
                                     msg=msg,
                                     messagetype=messagetype)
     def __library_ui(self, trans, request=None, **kwd):
+        '''
+        This method creates the data library & folder selectbox for new &
+        editing requests. First we get a list of all the libraries accessible to
+        the current user and display it in a selectbox. If the user has select an
+        existing library then display all the accessible sub folders of the selected 
+        data library. 
+        '''
         params = util.Params( kwd )
         lib_id = params.get( 'library_id', 'none'  )
-        # if editing a request
         selected_lib = None
+        # if editing a request and the user has already associated a library to
+        # this request, then set the selected_lib to the request.library
         if request and lib_id == 'none':
             if request.library:
                 lib_id = str(request.library.id)
                 selected_lib = request.library
-        else:
-            # new request
-            selected_lib = None
         # get all permitted libraries for this user
         all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \
                                                .order_by( trans.app.model.Library.name ).all()
@@ -497,15 +505,16 @@
             can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check )
             if can_show:
                 libraries[ library ] = hidden_folder_ids
+        # create data library selectbox with refresh on change enabled
         lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
         lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list )
-        # fill up the options in the Library selectfield
-        # first option
+        # fill up the options in the Library selectbox
+        # first option 'none' is the value for "Select one" option
         if lib_id == 'none':
             lib_list.add_option('Select one', 'none', selected=True)
         else:
             lib_list.add_option('Select one', 'none')
-        # all the libraries available to the user
+        # add all the libraries available to the user to the library selectbox
         for lib, hidden_folder_ids in libraries.items():
             if str(lib.id) == lib_id:
                 lib_list.add_option(lib.name, lib.id, selected=True)
@@ -524,14 +533,21 @@
                           helptext='Data library where the resultant dataset will be stored.')
         # show the folder widget only if the user has selected a valid library above
         if selected_lib:
-            # when editing a request
+            # when editing a request, either the user has already selected a subfolder or not
             if request:
                 if request.folder:
                     current_fid = request.folder.id
-                else:
-                    current_fid = request.library.root_folder.id
+                else: 
+                    # when a folder not yet associated with the request then the 
+                    # the current folder is set to the root_folder of the 
+                    # parent data library if present. 
+                    if request.library:
+                        current_fid = request.library.root_folder.id
+                    else:
+                        current_fid = params.get( 'folder_id', 'none'  )
             else:
                 current_fid = params.get( 'folder_id', 'none'  )
+            # create the folder selectbox
             folder_list = SelectField( 'folder_id')
             # first option
             if lib_id == 'none':
@@ -543,6 +559,7 @@
                                                                               selected_lib, 
                                                                               actions_to_check, 
                                                                               selected_hidden_folder_ids )
+            # add all the folders to the folder selectbox
             for f in showable_folders:
                 if str(f.id) == str(current_fid):
                     folder_list.add_option(f.name, f.id, selected=True)
@@ -568,8 +585,6 @@
         Validates the request entered by the user 
         '''
         empty_fields = []
-#        if not request.library:
-#            empty_fields.append('Data library')
         # check rest of the fields of the form
         for index, field in enumerate(request.type.request_form.fields):
             if field['required'] == 'required' and request.values.content[index] in ['', None]:
diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/web/controllers/requests_admin.py
--- a/lib/galaxy/web/controllers/requests_admin.py	Tue Oct 13 18:15:06 2009 -0400
+++ b/lib/galaxy/web/controllers/requests_admin.py	Wed Oct 14 02:22:11 2009 -0400
@@ -10,6 +10,10 @@
 from galaxy.web.controllers.forms import get_all_forms
log = logging.getLogger( __name__ )
+
+#
+# ---- Request Grid ------------------------------------------------------------ 
+#
class RequestsListGrid( grids.Grid ):
     title = "Sequencing Requests"
@@ -60,6 +64,11 @@
         else:
             return query
+
+#
+# ---- Request Controller ------------------------------------------------------ 
+#
+
 class Requests( BaseController ):
     request_grid = RequestsListGrid()
@@ -67,6 +76,7 @@
     @web.require_admin
     def index( self, trans ):
         return trans.fill_template( "/admin/requests/index.mako" )
+    
     @web.expose
     @web.require_admin
     def list( self, trans, **kwargs ):
@@ -104,51 +114,26 @@
         self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED)
         # Render the list view
         return self.request_grid( trans, **kwargs )
-    @web.expose
-    @web.require_admin
-    def edit(self, trans, **kwd):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
+    def __show_request(self, trans, id, messagetype, msg):
         try:
-            request = trans.app.model.Request.get(int(params.get('request_id', None)))
+            request = trans.app.model.Request.get(id)
         except:
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                               action='list',
                                                               status='error',
                                                               message="Invalid request ID",
                                                               **kwd) )
-        if params.get('show', False) == 'True':
-            return self.__edit_request(trans, request.id, **kwd)
-        elif params.get('save_changes_request_button', False) == 'Save changes' \
-             or params.get('edit_samples_button', False) == 'Edit samples':
-                request_type = trans.app.model.RequestType.get(int(params.select_request_type))
-                if not util.restore_text(params.get('name', '')):
-                    msg = 'Please enter the <b>Name</b> of the request'
-                    kwd['messagetype'] = 'error'
-                    kwd['msg'] = msg
-                    kwd['show'] = 'True'
-                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                      action='edit',
-                                                                      **kwd) )
-                request = self.__save_request(trans, request, **kwd)
-                msg = 'The changes made to the request named %s has been saved' % request.name
-                if params.get('save_changes_request_button', False) == 'Save changes':
-                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                      action='list',
-                                                                      message=msg ,
-                                                                      status='done') )
-                elif params.get('edit_samples_button', False) == 'Edit samples':
-                    new_kwd = {}
-                    new_kwd['request_id'] = request.id
-                    new_kwd['edit_samples_button'] = 'Edit samples'
-                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                      action='show_request',
-                                                                      msg=msg ,
-                                                                      messagetype='done',
-                                                                      **new_kwd) )
-        elif params.get('refresh', False) == 'true':
-            return self.__edit_request(trans, request.id, **kwd)
+        current_samples = []
+        for s in request.samples:
+            current_samples.append([s.name, s.values.content])
+        return trans.fill_template( '/admin/requests/show_request.mako',
+                                    request=request,
+                                    request_details=self.request_details(trans, id),
+                                    current_samples = current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details='hide', edit_mode='False',
+                                    msg=msg, messagetype=messagetype)
+
     def __edit_request(self, trans, id, **kwd):
         try:
             request = trans.app.model.Request.get(id)
@@ -276,317 +261,10 @@
                                                           action='list',
                                                           show_filter=trans.app.model.Request.states.SUBMITTED,
                                                           **kwd) )
-    @web.expose
-    @web.require_admin
-    def submit_request(self, trans, **kwd):
-        params = util.Params( kwd )
-        try:
-            id = int(params.get('id', False))
-            request = trans.app.model.Request.get(id)
-        except:
-            msg = "Invalid request ID"
-            log.warn( msg )
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message=msg,
-                                                              **kwd) )
-        msg = self.__validate(trans, request)
-        if msg:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='edit',
-                                                              messagetype='error',
-                                                              msg=msg,
-                                                              request_id=request.id,
-                                                              show='True') )
-        # get the new state
-        new_state = request.type.states[0]
-        for s in request.samples:
-            event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system')
-            event.flush()
-        # change request's submitted field
-        request.state = request.states.SUBMITTED
-        request.flush()
-        kwd['id'] = trans.security.encode_id(request.id)
-        kwd['status'] = 'done'
-        kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name
-        return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          show_filter=trans.app.model.Request.states.SUBMITTED,
-                                                          **kwd) )
-    def __copy_sample(self):
-        copy_list = SelectField('copy_sample')
-        copy_list.add_option('None', -1, selected=True)  
-        for i, s in enumerate(self.current_samples):
-            copy_list.add_option(s[0], i)
-        return copy_list   
-    def __update_samples(self, request, **kwd):
-        params = util.Params( kwd )
-        num_samples = len(self.current_samples)
-        self.current_samples = []
-        for s in request.samples:
-            self.current_samples.append([s.name, s.values.content])
-        for index in range(num_samples-len(request.samples)):
-            sample_index = index + len(request.samples)
-            sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-            sample_values = []
-            for field_index in range(len(request.type.sample_form.fields)):
-                sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-            self.current_samples.append([sample_name, sample_values])
-    def __show_request(self, trans, id, messagetype, msg):
-        try:
-            request = trans.app.model.Request.get(id)
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID",
-                                                              **kwd) )
-        self.current_samples = []
-        self.edit_mode = False
-        for s in request.samples:
-            self.current_samples.append([s.name, s.values.content])
-        self.details_state = 'Show request details'
-        return trans.fill_template( '/admin/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, id),
-                                    current_samples = self.current_samples, 
-                                    sample_copy=self.__copy_sample(), 
-                                    details_state=self.details_state,
-                                    edit_mode=self.edit_mode,
-                                    msg=msg, messagetype=messagetype)
-    @web.expose
-    @web.require_admin
-    def show_request(self, trans, **kwd):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        try:
-            request = trans.app.model.Request.get(int(params.get('request_id', None)))
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID",
-                                                              **kwd) )
-        if params.get('import_samples_button', False) == 'Import samples':
-            try:
-                file_obj = params.get('file_data', '')
-                import csv
-                reader = csv.reader(file_obj.file)
-                for row in reader:
-                    self.current_samples.append([row[0], row[1:]])  
-                return trans.fill_template( '/admin/requests/show_request.mako',
-                                            request=request,
-                                            request_details=self.request_details(trans, request.id),
-                                            current_samples=self.current_samples,
-                                            sample_copy=self.__copy_sample(), 
-                                            details_state=self.details_state,
-                                            edit_mode=self.edit_mode)
-            except:
-                return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                                  action='list',
-                                                                  status='error',
-                                                                  operation='show_request',
-                                                                  id=trans.security.encode_id(request.id),
-                                                                  message='Error in importing samples from the given file.',
-                                                                  **kwd))
-        elif params.get('add_sample_button', False) == 'Add New':
-            # save the all (saved+unsaved) sample info in 'current_samples'
-            self.__update_samples(request, **kwd)
-            # add an empty or filled sample
-            # if the user has selected a sample no. to copy then copy the contents 
-            # of the src sample to the new sample else an empty sample
-            src_sample_index = int(params.get( 'copy_sample', -1  ))
-            if src_sample_index == -1:
-                # empty sample
-                self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]])
-            else:
-                self.current_samples.append([self.current_samples[src_sample_index][0]+'_%i' % (len(self.current_samples)+1),
-                                                                  [val for val in self.current_samples[src_sample_index][1]]])
-            return trans.fill_template( '/admin/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=self.current_samples,
-                                        sample_copy=self.__copy_sample(), 
-                                        details_state=self.details_state,
-                                        edit_mode=self.edit_mode)
-        elif params.get('save_samples_button', False) == 'Save':
-            # update current_samples
-            self.__update_samples(request, **kwd)
-            # check for duplicate sample names
-            msg = ''
-            for index in range(len(self.current_samples)-len(request.samples)):
-                sample_index = index + len(request.samples)
-                sample_name = self.current_samples[sample_index][0]
-                if not sample_name.strip():
-                    msg = 'Please enter the name of sample number %i' % sample_index
-                    break
-                count = 0
-                for i in range(len(self.current_samples)):
-                    if sample_name == self.current_samples[i][0]:
-                        count = count + 1
-                if count > 1: 
-                    msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
-                    break
-            if msg:
-                return trans.fill_template( '/admin/requests/show_request.mako',
-                                            request=request,
-                                            request_details=self.request_details(trans, request.id),
-                                            current_samples = self.current_samples,
-                                            sample_copy=self.__copy_sample(), details_state=self.details_state,
-                                            messagetype='error', msg=msg)
-            # save all the new/unsaved samples entered by the user
-            if not self.edit_mode:
-                for index in range(len(self.current_samples)-len(request.samples)):
-                    sample_index = index + len(request.samples)
-                    sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-                    sample_values = []
-                    for field_index in range(len(request.type.sample_form.fields)):
-                        sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-                    form_values = trans.app.model.FormValues(request.type.sample_form, sample_values)
-                    form_values.flush()                    
-                    s = trans.app.model.Sample(sample_name, '', request, form_values)
-                    s.flush()
-            else:
-                for index in range(len(self.current_samples)):
-                    sample_index = index
-                    sample_name = self.current_samples[sample_index][0]
-                    new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-                    sample_values = []
-                    for field_index in range(len(request.type.sample_form.fields)):
-                        sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-                    sample = request.has_sample(sample_name)
-                    if sample:
-                        form_values = trans.app.model.FormValues.get(sample.values.id)
-                        form_values.content = sample_values
-                        form_values.flush()
-                        sample.name = new_sample_name
-                        sample.flush()
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          operation='show_request',
-                                                          id=trans.security.encode_id(request.id)) )
-        elif params.get('edit_samples_button', False) == 'Edit samples':
-            self.edit_mode = True
-            return trans.fill_template( '/admin/requests/show_request.mako',
-                                        request=request,
-                                        request_details=self.request_details(trans, request.id),
-                                        current_samples=self.current_samples,
-                                        sample_copy=self.__copy_sample(), 
-                                        details_state=self.details_state,
-                                        edit_mode=self.edit_mode)
-        elif params.get('cancel_changes_button', False) == 'Cancel':
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          operation='show_request',
-                                                          id=trans.security.encode_id(request.id)) )
-            
-    @web.expose
-    @web.require_admin
-    def delete_sample(self, trans, **kwd):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        request = trans.app.model.Request.get(int(params.get('request_id', 0)))
-        sample_index = int(params.get('sample_id', 0))
-        sample_name = self.current_samples[sample_index][0]
-        s = request.has_sample(sample_name)
-        if s:
-            s.delete()
-            s.flush()
-            request.flush()
-        del self.current_samples[sample_index]  
-        return trans.fill_template( '/admin/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples = self.current_samples,
-                                    sample_copy=self.__copy_sample(), 
-                                    details_state=self.details_state,
-                                    edit_mode=self.edit_mode)
-
-    @web.expose
-    @web.require_admin
-    def toggle_request_details(self, trans, **kwd):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        request = trans.app.model.Request.get(int(params.get('request_id', 0)))
-        if self.details_state == 'Show request details':
-             self.details_state = 'Hide request details'
-        elif self.details_state == 'Hide request details':
-             self.details_state = 'Show request details'
-        copy_list = SelectField('copy_sample')
-        copy_list.add_option('None', -1, selected=True)  
-        for i, s in enumerate(self.current_samples):
-            copy_list.add_option(i+1, i)    
-        return trans.fill_template( '/admin/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples = self.current_samples,
-                                    sample_copy=copy_list, details_state=self.details_state)
-    def request_details(self, trans, id):
-        '''
-        Shows the request details
-        '''
-        request = trans.app.model.Request.get(id)
-        # list of widgets to be rendered on the request form
-        request_details = []
-        # main details
-        request_details.append(dict(label='User', 
-                                    value=str(request.user.email), 
-                                    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='State', 
-                                    value=request.state, 
-                                    helptext=''))
-        request_details.append(dict(label='Date created', 
-                                    value=request.create_time, 
-                                    helptext=''))
-        # library associated
-        if request.library:
-			value=request.library.name
-        else:
-			value = None
-        request_details.append(dict(label='Data library', 
-                                    value=value, 
-                                    helptext='Data library where the resultant dataset will be stored'))
-        # folder associated
-        if request.folder:
-            value = request.folder.name
-        else:
-            value = None
-        request_details.append( dict( label='Data library folder', 
-                                      value=value, 
-                                      helptext='Data library folder where the resultant dataset will be stored' ) )
-
-        # form fields
-        for index, field in enumerate(request.type.request_form.fields):
-            if field['required']:
-                req = 'Required'
-            else:
-                req = 'Optional'
-            if field['type'] == 'AddressField':
-                if request.values.content[index]:
-                    request_details.append(dict(label=field['label'],
-                                                value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(),
-                                                helptext=field['helptext']+' ('+req+')'))
-                else:
-                    request_details.append(dict(label=field['label'],
-                                                value=None,
-                                                helptext=field['helptext']+' ('+req+')'))
-            else: 
-                request_details.append(dict(label=field['label'],
-                                            value=request.values.content[index],
-                                            helptext=field['helptext']+' ('+req+')'))
-        return request_details
-    
+#
+#---- Request Creation ----------------------------------------------------------
+#    
     def __select_request_type(self, trans, rtid):
         rt_ids = ['none']
         for rt in trans.app.model.RequestType.query().all():
@@ -723,21 +401,22 @@
         return select_user
def __library_ui(self, trans, user, request=None, **kwd):
-        """
-        Return a list of libraries for which user has the permission
-        to perform the LIBRARY_ADD action on any of it's folders
-        """
+        '''
+        This method creates the data library & folder selectbox for new &
+        editing requests. First we get a list of all the libraries accessible to
+        the current user and display it in a selectbox. If the user has select an
+        existing library then display all the accessible sub folders of the selected 
+        data library. 
+        '''
         params = util.Params( kwd )
         lib_id = params.get( 'library_id', 'none'  )
-        # if editing a request
+        # if editing a request and the user has already associated a library to
+        # this request, then set the selected_lib to the request.library
         selected_lib = None
         if request and lib_id == 'none':
             if request.library:
                 lib_id = str(request.library.id)
                 selected_lib = request.library
-        else:
-            # new request
-            selected_lib = None
         # if new request no user is selected initially, none of the libraries are 
         # listed in the selectfield
         if not user:
@@ -759,10 +438,11 @@
                 can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check )
                 if can_show:
                     libraries[ library ] = hidden_folder_ids
-        # create the selectfield
+        # create data library selectbox with refresh on change enabled
         lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
         lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list )
-        # first option
+        # fill up the options in the Library selectbox
+        # first option 'none' is the value for "Select one" option
         if lib_id == 'none':
             lib_list.add_option('Select one', 'none', selected=True)
         else:
@@ -784,15 +464,23 @@
         lib_widget = dict(label='Data library', 
                           widget=lib_list, 
                           helptext='Data library where the resultant dataset will be stored.')
+        # show the folder widget only if the user has selected a valid library above
         if selected_lib:
-            # when editing a request
+            # when editing a request, either the user has already selected a subfolder or not
             if request:
                 if request.folder:
                     current_fid = request.folder.id
-                else:
-                    current_fid = request.library.root_folder.id
+                else: 
+                    # when a folder not yet associated with the request then the 
+                    # the current folder is set to the root_folder of the 
+                    # parent data library if present. 
+                    if request.library:
+                        current_fid = request.library.root_folder.id
+                    else:
+                        current_fid = params.get( 'folder_id', 'none'  )
             else:
                 current_fid = params.get( 'folder_id', 'none'  )
+            # create the folder selectbox
             folder_list = SelectField( 'folder_id')
             # first option
             if lib_id == 'none':
@@ -828,9 +516,14 @@
         '''
         Validates the request entered by the user 
         '''
+        if not request.samples:
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              operation='show_request',
+                                                              message='Please add one or more samples to this request before submitting.',
+                                                              status='error',
+                                                              id=trans.security.encode_id(request.id)) )
         empty_fields = []
-#        if not request.library:
-#            empty_fields.append('Library')
         # check rest of the fields of the form
         for index, field in enumerate(request.type.request_form.fields):
             if field['required'] == 'required' and request.values.content[index] in ['', None]:
@@ -909,6 +602,350 @@
             request.folder = folder
             request.flush()
         return request
+
+
+#
+#---- Request Editing ----------------------------------------------------------
+#    
+    @web.expose
+    @web.require_admin
+    def edit(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        try:
+            request = trans.app.model.Request.get(int(params.get('request_id', None)))
+        except:
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid request ID",
+                                                              **kwd) )
+        if params.get('show', False) == 'True':
+            return self.__edit_request(trans, request.id, **kwd)
+        elif params.get('save_changes_request_button', False) == 'Save changes' \
+             or params.get('edit_samples_button', False) == 'Edit samples':
+                request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+                if not util.restore_text(params.get('name', '')):
+                    msg = 'Please enter the <b>Name</b> of the request'
+                    kwd['messagetype'] = 'error'
+                    kwd['msg'] = msg
+                    kwd['show'] = 'True'
+                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                                      action='edit',
+                                                                      **kwd) )
+                request = self.__save_request(trans, request, **kwd)
+                msg = 'The changes made to the request named %s has been saved' % request.name
+                if params.get('save_changes_request_button', False) == 'Save changes':
+                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                                      action='list',
+                                                                      message=msg ,
+                                                                      status='done') )
+                elif params.get('edit_samples_button', False) == 'Edit samples':
+                    new_kwd = {}
+                    new_kwd['request_id'] = request.id
+                    new_kwd['edit_samples_button'] = 'Edit samples'
+                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                                      action='show_request',
+                                                                      msg=msg ,
+                                                                      messagetype='done',
+                                                                      **new_kwd) )
+        elif params.get('refresh', False) == 'true':
+            return self.__edit_request(trans, request.id, **kwd)
+    @web.expose
+    @web.require_admin
+    def submit_request(self, trans, **kwd):
+        params = util.Params( kwd )
+        try:
+            id = int(params.get('id', False))
+            request = trans.app.model.Request.get(id)
+        except:
+            msg = "Invalid request ID"
+            log.warn( msg )
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              status='error',
+                                                              message=msg,
+                                                              **kwd) )
+        msg = self.__validate(trans, request)
+        if msg:
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='edit',
+                                                              messagetype='error',
+                                                              msg=msg,
+                                                              request_id=request.id,
+                                                              show='True') )
+        # get the new state
+        new_state = request.type.states[0]
+        for s in request.samples:
+            event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system')
+            event.flush()
+        # change request's submitted field
+        request.state = request.states.SUBMITTED
+        request.flush()
+        kwd['id'] = trans.security.encode_id(request.id)
+        kwd['status'] = 'done'
+        kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name
+        return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                          action='list',
+                                                          show_filter=trans.app.model.Request.states.SUBMITTED,
+                                                          **kwd) )
+    def __update_samples(self, request, **kwd):
+        '''
+        This method retrieves all the user entered sample information and
+        returns an list of all the samples and their field values
+        '''
+        params = util.Params( kwd )
+        current_samples = []
+        for s in request.samples:
+            current_samples.append([s.name, s.values.content])
+        index = len(request.samples) 
+        while True:
+            if params.get( 'sample_%i_name' % index, ''  ):
+                sample_index = index
+                sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
+                sample_values = []
+                for field_index in range(len(request.type.sample_form.fields)):
+                    sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
+                current_samples.append([sample_name, sample_values])
+                index = index + 1
+            else:
+                break
+        details = params.get( 'details', 'hide' )
+        edit_mode = params.get( 'edit_mode', 'False' )
+        return current_samples, details, edit_mode
+    def __copy_sample(self, current_samples):
+        copy_list = SelectField('copy_sample')
+        copy_list.add_option('None', -1, selected=True)  
+        for i, s in enumerate(current_samples):
+            copy_list.add_option(s[0], i)
+        return copy_list   
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def show_request(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        try:
+            request = trans.app.model.Request.get(int(params.get('request_id', None)))
+        except:
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid request ID",
+                                                              **kwd) )
+        # get the user entered sample details
+        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
+        if params.get('import_samples_button', False) == 'Import samples':
+            try:
+                file_obj = params.get('file_data', '')
+                import csv
+                reader = csv.reader(file_obj.file)
+                for row in reader:
+                    current_samples.append([row[0], row[1:]])  
+                return trans.fill_template( '/admin/requests/show_request.mako',
+                                            request=request,
+                                            request_details=self.request_details(trans, request.id),
+                                            current_samples=current_samples,
+                                            sample_copy=self.__copy_sample(current_samples), 
+                                            details=details,
+                                            edit_mode=edit_mode)
+            except:
+                return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                                  action='list',
+                                                                  status='error',
+                                                                  message='Error in importing samples file',
+                                                                  **kwd))
+        elif params.get('add_sample_button', False) == 'Add New':
+            # add an empty or filled sample
+            # if the user has selected a sample no. to copy then copy the contents 
+            # of the src sample to the new sample else an empty sample
+            src_sample_index = int(params.get( 'copy_sample', -1  ))
+            if src_sample_index == -1:
+                # empty sample
+                current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
+            else:
+                current_samples.append([current_samples[src_sample_index][0]+'_%i' % (len(current_samples)+1),
+                                                                  [val for val in current_samples[src_sample_index][1]]])
+            return trans.fill_template( '/admin/requests/show_request.mako',
+                                        request=request,
+                                        request_details=self.request_details(trans, request.id),
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details,
+                                        edit_mode=edit_mode)
+        elif params.get('save_samples_button', False) == 'Save':
+            # check for duplicate sample names
+            msg = ''
+            for index in range(len(current_samples)-len(request.samples)):
+                sample_index = index + len(request.samples)
+                sample_name = current_samples[sample_index][0]
+                if not sample_name.strip():
+                    msg = 'Please enter the name of sample number %i' % sample_index
+                    break
+                count = 0
+                for i in range(len(current_samples)):
+                    if sample_name == current_samples[i][0]:
+                        count = count + 1
+                if count > 1: 
+                    msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
+                    break
+            if msg:
+                return trans.fill_template( '/admin/requests/show_request.mako',
+                                            request=request,
+                                            request_details=self.request_details(trans, request.id),
+                                            current_samples = current_samples,
+                                            sample_copy=self.__copy_sample(current_samples), 
+                                            details=details, edit_mode=edit_mode,
+                                            messagetype='error', msg=msg)
+            # save all the new/unsaved samples entered by the user
+            if edit_mode == 'False':
+                for index in range(len(current_samples)-len(request.samples)):
+                    sample_index = index + len(request.samples)
+                    sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
+                    sample_values = []
+                    for field_index in range(len(request.type.sample_form.fields)):
+                        sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
+                    form_values = trans.app.model.FormValues(request.type.sample_form, sample_values)
+                    form_values.flush()                    
+                    s = trans.app.model.Sample(sample_name, '', request, form_values)
+                    s.flush()
+            else:
+                for index in range(len(current_samples)):
+                    sample_index = index
+                    sample_name = current_samples[sample_index][0]
+                    new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
+                    sample_values = []
+                    for field_index in range(len(request.type.sample_form.fields)):
+                        sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
+                    sample = request.has_sample(sample_name)
+                    if sample:
+                        form_values = trans.app.model.FormValues.get(sample.values.id)
+                        form_values.content = sample_values
+                        form_values.flush()
+                        sample.name = new_sample_name
+                        sample.flush()
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                          action='list',
+                                                          operation='show_request',
+                                                          id=trans.security.encode_id(request.id)) )
+        elif params.get('edit_samples_button', False) == 'Edit samples':
+            edit_mode = 'True'
+            return trans.fill_template( '/admin/requests/show_request.mako',
+                                        request=request,
+                                        request_details=self.request_details(trans, request.id),
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details,
+                                        edit_mode=edit_mode)
+        elif params.get('cancel_changes_button', False) == 'Cancel':
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                          action='list',
+                                                          operation='show_request',
+                                                          id=trans.security.encode_id(request.id)) )
+
+            
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def delete_sample(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        request = trans.app.model.Request.get(int(params.get('request_id', 0)))
+        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
+        sample_index = int(params.get('sample_id', 0))
+        sample_name = current_samples[sample_index][0]
+        s = request.has_sample(sample_name)
+        if s:
+            s.delete()
+            s.flush()
+            request.flush()
+        del current_samples[sample_index]  
+        return trans.fill_template( '/admin/requests/show_request.mako',
+                                    request=request,
+                                    request_details=self.request_details(trans, request.id),
+                                    current_samples = current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details=details,
+                                    edit_mode=edit_mode)
+        
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def toggle_request_details(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        request = trans.app.model.Request.get(int(params.get('request_id', 0)))
+        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
+        return trans.fill_template( '/admin/requests/show_request.mako',
+                                    request=request,
+                                    request_details=self.request_details(trans, request.id),
+                                    current_samples = current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details=details,
+                                    edit_mode=edit_mode)
+    @web.expose
+    @web.require_admin
+    def request_details(self, trans, id):
+        '''
+        Shows the request details
+        '''
+        request = trans.app.model.Request.get(id)
+        # list of widgets to be rendered on the request form
+        request_details = []
+        # main details
+        request_details.append(dict(label='User', 
+                                    value=str(request.user.email), 
+                                    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='State', 
+                                    value=request.state, 
+                                    helptext=''))
+        request_details.append(dict(label='Date created', 
+                                    value=request.create_time, 
+                                    helptext=''))
+        # library associated
+        if request.library:
+			value=request.library.name
+        else:
+			value = None
+        request_details.append(dict(label='Data library', 
+                                    value=value, 
+                                    helptext='Data library where the resultant dataset will be stored'))
+        # folder associated
+        if request.folder:
+            value = request.folder.name
+        else:
+            value = None
+        request_details.append( dict( label='Data library folder', 
+                                      value=value, 
+                                      helptext='Data library folder where the resultant dataset will be stored' ) )
+
+        # form fields
+        for index, field in enumerate(request.type.request_form.fields):
+            if field['required']:
+                req = 'Required'
+            else:
+                req = 'Optional'
+            if field['type'] == 'AddressField':
+                if request.values.content[index]:
+                    request_details.append(dict(label=field['label'],
+                                                value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(),
+                                                helptext=field['helptext']+' ('+req+')'))
+                else:
+                    request_details.append(dict(label=field['label'],
+                                                value=None,
+                                                helptext=field['helptext']+' ('+req+')'))
+            else: 
+                request_details.append(dict(label=field['label'],
+                                            value=request.values.content[index],
+                                            helptext=field['helptext']+' ('+req+')'))
+        return request_details
     @web.expose
     @web.require_admin
     def bar_codes(self, trans, **kwd):
@@ -1086,7 +1123,9 @@
                                     events_list=events_list,
                                     sample=sample, widgets=widgets, title=title)
-    # Request Type Stuff
+##
+#### Request Type Stuff ###################################################
+##
     @web.expose
     @web.require_admin
     def manage_request_types( self, trans, **kwd ):       
diff -r b16a6d767e65 -r ca816e66ec69 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py	Tue Oct 13 18:15:06 2009 -0400
+++ b/lib/galaxy/web/framework/__init__.py	Wed Oct 14 02:22:11 2009 -0400
@@ -635,7 +635,7 @@
         return None
def request_types(self):
-        if self.app.model.RequestType.query().all():
+        if self.app.model.RequestType.query().filter_by(deleted=False).all():
             return True
         return False
diff -r b16a6d767e65 -r ca816e66ec69 templates/admin/forms/edit_form.mako
--- a/templates/admin/forms/edit_form.mako	Tue Oct 13 18:15:06 2009 -0400
+++ b/templates/admin/forms/edit_form.mako	Wed Oct 14 02:22:11 2009 -0400
@@ -36,16 +36,20 @@
             <% options = field_attr[2] %>
             <div class="repeat-group-item">
                 <div class="form-row">
-                <label> Options</label>
-                %for i, option in enumerate(options):
-                    <b> ${i+1}</b>
-                    ${option[1].get_html()}                    
-                    <a class="action-button" href="${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
+                    <label> Options</label>
+                    %for i, option in enumerate(options):
+                        <div class="form-row">
+                            <b> ${i+1}</b>
+                            ${option[1].get_html()}
+                            ##<a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='remove', field_index=index, option_index=i )}">Remove</a><br>                            
+                            <input type="submit" name="removeoption_${index}_${i}" value="Remove"/>
+                        </div>
+                    %endfor
+                    <input type="hidden" name="field_index" value="${index}"/>
                 </div>
             </div>
             <div class="form-row">
-                <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='add', field_index=index )}">Add</a>
+                <input type="submit" name="addoption_${index}" value="Add"/>
             </div>
         %endif
     %endif
@@ -81,7 +85,7 @@
<div class="toolForm">
     <div class="toolFormTitle">Edit form definition "${form.name}"</div>
-    <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id, num_fields=len(form.fields)  )}" method="post" >
+    <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id  )}" method="post" >
         %for label, input in form_details:
             <div class="form-row">
                 <label>${label}</label>
diff -r b16a6d767e65 -r ca816e66ec69 templates/admin/forms/show_form_read_only.mako
--- a/templates/admin/forms/show_form_read_only.mako	Tue Oct 13 18:15:06 2009 -0400
+++ b/templates/admin/forms/show_form_read_only.mako	Wed Oct 14 02:22:11 2009 -0400
@@ -63,9 +63,19 @@
<div class="toolForm">
     %if form.desc:
-        <div class="toolFormTitle">${form.name} - <i>${form.desc}</i></div>
+        <div class="toolFormTitle">${form.name} - <i>${form.desc}</i>
+            <a id="form-${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</a>
+            </div>
+        </div>
     %else:
-        <div class="toolFormTitle">${form.name}</div>
+        <div class="toolFormTitle">${form.name}
+        <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="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit</a>
+        </div>
+        </div>
     %endif
     <form name="library" action="${h.url_for( controller='forms', action='manage' )}" method="post" >
         %if form.type == trans.app.model.FormDefinition.types.SAMPLE:
@@ -77,58 +87,27 @@
                 %endfor
             %endif
         %else:
-            <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>${field['required']}</a>
-                                </div>
-                            </td>
-                        </tr>       
-                    %endfor
-                </tbody>
-            </table>
+            %for index, field in enumerate(form.fields):
+                <div class="form-row">
+                    <label>${field['label']}</label>
+                    %if field['helptext']:
+                        <div class="toolParamHelp" style="clear: both;">
+                            <i>${field['helptext']}</i>
+                        </div>
+                    %endif
+                    <div>${field['required']}</div>
+                    <i>Type: </i> ${field['type']}
+                    %if field['type'] == 'SelectField':
+                        <div>
+                        <div><i>Options:</i></div>
+                        %for option in field['selectlist']:
+                            <div>${option}</div>
+                        %endfor
+                        </div>
+                    %endif
+                </div>
+                <div style="clear: both"></div>
+            %endfor
         %endif
     </form>
     </div>
diff -r b16a6d767e65 -r ca816e66ec69 templates/admin/requests/show_request.mako
--- a/templates/admin/requests/show_request.mako	Tue Oct 13 18:15:06 2009 -0400
+++ b/templates/admin/requests/show_request.mako	Wed Oct 14 02:22:11 2009 -0400
@@ -58,6 +58,8 @@
                 </select>
             %elif field['type'] == 'CheckboxField':
                 <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
+            %elif field['type'] == 'NumberField':
+                <input type=int name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
             %endif
             <div class="toolParamHelp" style="clear: both;">
                 <i>${'('+field['required']+')' }</i>
@@ -91,35 +93,41 @@
 </%def>
<div class="toolForm">
-        <div class="form-row">
-        <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id )}">${details_state}</a>
-        </div>
-        %if details_state == "Hide request details":
-            %for index, rd in enumerate(request_details):
+    <div class="form-row">
+        %if details == "show":
+            <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id, details="hide"  )}">Hide request details</a>
+            </div>
+                %for index, rd in enumerate(request_details):
+                    <div class="form-row">
+                        <label>${rd['label']}</label>
+                        %if not rd['value']:
+                            <i>None</i>
+                        %else:                      
+                            %if rd['label'] == 'Data library':
+                                %if rd['value']:
+                                    <a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
+                                %else:
+                                    <i>None</i>
+                                %endif
+                            %else:
+                                ${rd['value']}     
+                            %endif
+                        %endif
+                    </div>
+                    <div style="clear: both"></div>
+                %endfor
                 <div class="form-row">
-                    <label>${rd['label']}</label>
-                    %if not rd['value']:
-                        <i>None</i>
-                    %else:                      
-                        %if rd['label'] == 'Data library':
-                            <a href="${h.url_for( controller='library_admin', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
-                        %else:
-                            ${rd['value']}     
-                        %endif
-                    %endif
-                </div>
-                <div style="clear: both"></div>
-            %endfor
-            <div class="form-row">
                 <ul class="manage-table-actions">
                     <li>
                         <a class="action-button"  href="${h.url_for( controller='requests_admin', action='edit', show=True, request_id=request.id)}">
                         <span>Edit request details</span></a>
                     </li>
                 </ul>
+                </div>
             </div>
+        %else:
+            <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id, details="show"  )}">Show request details</a>        
         %endif
-    </div>
 </div>
<%def name="render_grid( grid_index, grid_name, fields_dict )">
@@ -151,13 +159,13 @@
             request.refresh()
             %>
             %for sample_index, sample in enumerate(current_samples):
-                %if edit_mode:
+                %if edit_mode == 'True':
                     <tr>
                         <td>${sample_index+1}</td>
                         ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)}
                         <td>
                             %if request.unsubmitted() and grid_index == 0:
-                                <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
+                                <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
                                 <img src="${h.url_for('/static/images/delete_icon.png')}" />
                                 <span></span></a>
                             %endif
@@ -173,7 +181,7 @@
                         %endif
                         <td>
                             %if request.unsubmitted() and grid_index == 0:
-                                <a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
+                                <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
                                 <img src="${h.url_for('/static/images/delete_icon.png')}" />
                                 <span></span></a>
                             %endif
@@ -201,7 +209,7 @@
                 <label>There are no samples.</label>
             %endif
         </div>
-        %if not edit_mode:
+        %if edit_mode == 'False':
             <table class="grid">
                 <tbody>
                     <tr>
@@ -238,7 +246,7 @@
               <div style="clear: both"></div>
             </div>
             <div class="form-row">
-                %if edit_mode:   
+                %if edit_mode == 'True':   
                     <input type="submit" name="save_samples_button" value="Save"/>
                     <input type="submit" name="cancel_changes_button" value="Cancel"/>
                 %elif request.unsubmitted():
diff -r b16a6d767e65 -r ca816e66ec69 templates/requests/show_request.mako
--- a/templates/requests/show_request.mako	Tue Oct 13 18:15:06 2009 -0400
+++ b/templates/requests/show_request.mako	Wed Oct 14 02:22:11 2009 -0400
@@ -92,41 +92,43 @@
 </%def>
<div class="toolForm">
-        <div class="form-row">
-        <a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id )}">${details_state}</a>
-        </div>
-        %if details_state == "Hide request details":
-            %for index, rd in enumerate(request_details):
-                <div class="form-row">
-                    <label>${rd['label']}</label>
-                    %if not rd['value']:
-                        <i>None</i>
-                    %else:                      
-                        %if rd['label'] == 'Data library':
-                            %if rd['value']:
-                                <a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
+    <div class="form-row">
+        %if details == "show":
+            <a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id, details="hide"  )}">Hide request details</a>
+            </div>
+                %for index, rd in enumerate(request_details):
+                    <div class="form-row">
+                        <label>${rd['label']}</label>
+                        %if not rd['value']:
+                            <i>None</i>
+                        %else:                      
+                            %if rd['label'] == 'Data library':
+                                %if rd['value']:
+                                    <a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
+                                %else:
+                                    <i>None</i>
+                                %endif
                             %else:
-                                <i>None</i>
+                                ${rd['value']}     
                             %endif
-                        %else:
-                            ${rd['value']}     
                         %endif
-                    %endif
-                </div>
-                <div style="clear: both"></div>
-            %endfor
-            %if request.unsubmitted():
-                <div class="form-row">
-                <ul class="manage-table-actions">
-                    <li>
-                        <a class="action-button"  href="${h.url_for( controller='requests', action='edit', show=True, request_id=request.id)}">
-                        <span>Edit request details</span></a>
-                    </li>
-                </ul>
-                </div>
-            %endif
+                    </div>
+                    <div style="clear: both"></div>
+                %endfor
+                %if request.unsubmitted():
+                    <div class="form-row">
+                    <ul class="manage-table-actions">
+                        <li>
+                            <a class="action-button"  href="${h.url_for( controller='requests', action='edit', show=True, request_id=request.id)}">
+                            <span>Edit request details</span></a>
+                        </li>
+                    </ul>
+                    </div>
+                %endif
+            </div>
+        %else:
+            <a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id, details="show"  )}">Show request details</a>        
         %endif
-    </div>
 </div>
<%def name="render_grid( grid_index, grid_name, fields_dict )">
@@ -158,7 +160,7 @@
             request.refresh()
             %>
             %for sample_index, sample in enumerate(current_samples):
-                %if edit_mode:
+                %if edit_mode == 'True':
                     <tr>
                         <td>${sample_index+1}</td>
                         ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)}
@@ -194,7 +196,7 @@
<div class="toolForm">
     ##<div class="toolFormTitle">Samples (${len(request.samples)})</div>
-    <form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request' )}" enctype="multipart/form-data" method="post" >
+    <form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
         <div class="form-row">
             %if current_samples:
                 %if not request.type.sample_form.layout:
@@ -211,7 +213,7 @@
             %endif
</div>
-        %if request.unsubmitted() and not edit_mode:
+        %if request.unsubmitted() and edit_mode == 'False':
         <table class="grid">
             <tbody>
                 <tr>
@@ -251,7 +253,7 @@
             </div>
             <div class="form-row">
                 <input type="submit" name="save_samples_button" value="Save"/>
-                %if edit_mode:                    
+                %if edit_mode == 'True':
                     <input type="submit" name="cancel_changes_button" value="Cancel"/>
                 %endif
             </div>
diff -r b16a6d767e65 -r ca816e66ec69 templates/user/address.mako
--- a/templates/user/address.mako	Tue Oct 13 18:15:06 2009 -0400
+++ b/templates/user/address.mako	Wed Oct 14 02:22:11 2009 -0400
@@ -46,7 +46,7 @@
                                 <td>
                                     <div class="form-row">   
                                         <label>${address.desc}</label>
-                                        ${address.display()}
+                                        ${address.get_html()}
                                     </div>
                                     <div class="form-row">
                                         <ul class="manage-table-actions">
diff -r b16a6d767e65 -r ca816e66ec69 test/base/twilltestcase.py
--- a/test/base/twilltestcase.py	Tue Oct 13 18:15:06 2009 -0400
+++ b/test/base/twilltestcase.py	Wed Oct 14 02:22:11 2009 -0400
@@ -1059,8 +1059,15 @@
             tc.fv( "1", field_name, field_contents )
             tc.fv( "1", field_help_name, field_help_contents )
             tc.submit( "save_changes_button" )
+        if num_fields:
             check_str = "The form '%s' has been updated with the changes." % name
-        self.check_page_for_string( check_str )
+            self.check_page_for_string( check_str )
+        else:
+            self.home()
+            self.visit_url( "%s/forms/manage" % self.url )
+            self.check_page_for_string( name )
+            self.check_page_for_string( desc )
+            self.check_page_for_string( formtype )
         self.home()
     def edit_form( self, form_id, form_name, new_form_name="Form One's Name (Renamed)", new_form_desc="This is Form One's description (Re-described)"):
         """
@@ -1074,7 +1081,7 @@
         tc.submit( "save_changes_button" )
         self.check_page_for_string( "The form '%s' has been updated with the changes." % new_form_name )
         self.home()
-    def form_add_field( self, form_id, form_name, field_index, fields):
+    def form_add_field( self, form_id, form_name, form_desc, form_type, field_index, fields):
         """
         Add a new fields to the form definition
         """
@@ -1088,13 +1095,18 @@
             tc.fv( "1", "field_helptext_%i" % index, field['desc'] )
             tc.fv( "1", "field_type_%i" % index, field['type'] )
             tc.fv( "1", "field_required_%i" % index, field['required'] )
-#            if field['type'] == 'SelectField':
-#                for option_index, option in enumerate(field['selectlist']):
-#                    self.visit_url( "%s/forms/edit?select_box_options=add&form_id=%i&field_index=%i" % \
-#                                    (self.url, form_id, index))
-#                    #data = self.last_page()
-#                    #file( "rc.html", 'wb' ).write(data)
-#                    tc.fv( "1", "field_%i_option_%i" % (index, option_index), option )
+            if field['type'] == 'SelectField':
+                options = ''
+                for option_index, option in enumerate(field['selectlist']):
+                    url_str = "%s/forms/edit?description=%s&form_id=%i&form_type_selectbox=%s&addoption_%i=Add&name=%s&field_name_%i=%s&field_helptext_%i=%s&field_type_%i=%s" % \
+                              (self.url, form_desc.replace(" ", "+"), form_id, form_type.replace(" ", "+"), 
+                               index, form_name.replace(" ", "+"), index, field['name'].replace(" ", "+"), 
+                               index, field['desc'].replace(" ", "+"), index, field['type'])
+                    self.visit_url( url_str + options )
+                    data = self.last_page()
+                    file( "rc.html", 'wb' ).write(data)
+                    tc.fv( "1", "field_%i_option_%i" % (index, option_index), option )
+                    options = options + "&field_%i_option_%i=%s" % (index, option_index, option)
         tc.submit( "save_changes_button" )
         check_str = "The form '%s' has been updated with the changes." % form_name
         self.check_page_for_string( check_str )
@@ -1130,18 +1142,22 @@
         self.check_page_for_string( "Request type <b>%s</b> has been created" % name )
     def create_request( self, request_type_id, name, desc, library_id, folder_id, fields ):
         self.home()
-        self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % (self.url, request_type_id) )
+        self.visit_url( "%s/requests/new?create=True&select_request_type=%i&library_id=%i" % ( self.url, 
+                                                                                               request_type_id,
+                                                                                               library_id ) )
         self.check_page_for_string( 'Add a new request' )
         tc.fv( "1", "name", name )
         tc.fv( "1", "desc", desc )
         tc.fv( "1", "library_id", str(library_id) )
-        #tc.fv( "1", "folder_id", str(folder_id) )
+        tc.fv( "1", "folder_id", str(folder_id) )
         for index, field_value in enumerate(fields):
             tc.fv( "1", "field_%i" % index, field_value )
         tc.submit( "create_request_button" )
     def create_request_admin( self, request_type_id, user_id, name, desc, library_id, fields ):
         self.home()
-        self.visit_url( "%s/requests_admin/new?create=True&select_request_type=%i" % (self.url, request_type_id) )
+        self.visit_url( "%s/requests_admin/new?create=True&select_request_type=%i&library_id=%i" % ( self.url, 
+                                                                                                     request_type_id,
+                                                                                                     library_id ) )
         self.check_page_for_string( 'Add a new request' )
         tc.fv( "1", "select_user", str(user_id) )
         tc.fv( "1", "name", name )
diff -r b16a6d767e65 -r ca816e66ec69 test/functional/test_forms_and_requests.py
--- a/test/functional/test_forms_and_requests.py	Tue Oct 13 18:15:06 2009 -0400
+++ b/test/functional/test_forms_and_requests.py	Wed Oct 14 02:22:11 2009 -0400
@@ -42,12 +42,7 @@
         name = form_one_name
         desc = "This is Form One's description"
         formtype = galaxy.model.FormDefinition.types.REQUEST
-        self.create_form( name=name, desc=desc, formtype=formtype )
-        self.home()
-        self.visit_page( 'forms/manage' )
-        self.check_page_for_string( name )
-        self.check_page_for_string( desc )
-        self.check_page_for_string( formtype )
+        self.create_form( name=name, desc=desc, formtype=formtype, num_fields=0 )
         # Get the form_definition object for later tests
         form_one = galaxy.model.FormDefinition.filter( and_( galaxy.model.FormDefinition.table.c.name==name,
                                                              galaxy.model.FormDefinition.table.c.desc==desc,
@@ -66,24 +61,21 @@
         """Testing adding fields to a form definition"""
         fields = [dict(name='Test field name one',
                        desc='Test field description one',
-                       type='TextField',
-                       required='required'),
+                       type='SelectField',
+                       required='optional',
+                       selectlist=['option1', 'option2']),
                   dict(name='Test field name two',
                        desc='Test field description two',
                        type='AddressField',
-                       required='optional')]
+                       required='optional'),
+                  dict(name='Test field name three',
+                       desc='Test field description three',
+                       type='TextField',
+                       required='required')]
         form_one = get_latest_form(form_one_name)
-        self.form_add_field(form_one.id, form_one.name, field_index=len(form_one.fields), fields=fields)
+        self.form_add_field(form_one.id, form_one.name, form_one.desc, form_one.type, field_index=len(form_one.fields), fields=fields)
         form_one_latest = get_latest_form(form_one_name)        
         assert len(form_one_latest.fields) == len(form_one.fields)+len(fields)
-#This following test has been commented out as it is causing:
-#TwillException: multiple matches to "remove_button"     
-#    def test_010_remove_form_fields( self ):
-#        """Testing removing fields from a form definition"""
-#        form_one = get_latest_form(form_one_name)
-#        self.form_remove_field( form_one.id, form_one.name, 'Test field name one' )
-#        form_one_latest = get_latest_form(form_one_name)
-#        assert len(form_one_latest.fields) == len(form_one.fields)-1
     def test_015_create_sample_form( self ):
         """Testing creating another form (for samples)"""
         global form_two_name
@@ -186,10 +178,10 @@
         self.logout()
         self.login( email='test1@bx.psu.edu' )
         # set field values
-        fields = ['field one value', 'field two value', str(user_address.id)] 
+        fields = ['option1', str(user_address.id), 'field three value'] 
         # create the request
         request_name, request_desc = 'Request One', 'Request One Description'
-        self.create_request(request_type.id, request_name, request_desc, library_one.id, folder_one.id, fields)
+        self.create_request(request_type.id, request_name, request_desc, library_one.id, 'none', fields)
         self.check_page_for_string( request_name )
         self.check_page_for_string( request_desc )
         global request_one
@@ -208,8 +200,9 @@
             for field_value in fields:
                 self.check_page_for_string( field_value )
         # edit this request
-        fields = ['field one value (edited)', 'field two value (edited)', str(user_address.id)]
-        self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields)
+        fields = ['option2', str(user_address.id), 'field three value (edited)'] 
+        self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', 
+                          request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields)
         request_one.refresh()
         self.check_page_for_string( request_name+' (Renamed)' )
         self.check_page_for_string( request_desc+' (Re-described)' )
@@ -261,8 +254,8 @@
         self.login( email='test@bx.psu.edu' )
         request_name = "RequestTwo"
         # simulate request creation
-        url_str = '%s/requests_admin/new?create=True&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&library_id=%i&folder_id=%i&refresh=True&field_1=%s&field_2=%i' \
-                  % ( self.url, request_type.id, regular_user.id, request_name, library_one.id, library_one.root_folder.id, "field_1_value", user_address.id )
+        url_str = '%s/requests_admin/new?create=True&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&library_id=%i&folder_id=%i&refresh=True&field_2=%s&field_0=%s&field_1=%i' \
+                  % ( self.url, request_type.id, regular_user.id, request_name, library_one.id, library_one.root_folder.id, "field_2_value", 'option1', user_address.id )
         self.home()
         self.visit_url( url_str )
         self.check_page_for_string( "The new request named %s has been created" % request_name )
@@ -299,10 +292,3 @@
         self.visit_url( '%s/requests_admin/list?show_filter=All' % self.url )
         self.check_page_for_string( request_one.name )
         self.check_page_for_string( request_two.name )
-
-        
-        
-        
-        
-        
-        
\ No newline at end of file

    

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[galaxy-dev] [hg] galaxy 2882: Forms & request controllers