[galaxy-dev] [hg] galaxy 2606: Merge

24 Aug 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/e6dda627e6b0
changeset: 2606:e6dda627e6b0
user:      James Taylor james@jamestaylor.org
date:      Sat Aug 22 23:20:09 2009 -0400
description:
Merge
2 file(s) affected in this change:
templates/base_panels.mako
templates/history/grid.mako
diffs (2711 lines):
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/model/migrate/versions/0009_request_table.py

--- a/lib/galaxy/model/migrate/versions/0009_request_table.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/model/migrate/versions/0009_request_table.py	Sat Aug 22 23:20:09 2009 -0400
@@ -9,6 +9,7 @@
 from migrate.changeset import *
 import sys, logging
 from galaxy.model.custom_types import *
+from sqlalchemy.exceptions import *
log = logging.getLogger( __name__ )
 log.setLevel(logging.DEBUG)
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/tools/__init__.py	Sat Aug 22 23:20:09 2009 -0400
@@ -1534,10 +1534,19 @@
                 child_dataset.flush()
                 child_dataset.set_size()
                 child_dataset.name = "Secondary Dataset (%s)" % ( designation )
-                child_dataset.state = child_dataset.states.OK
                 child_dataset.init_meta()
                 child_dataset.set_meta()
                 child_dataset.set_peek()
+                # Associate new dataset with job
+                job = None
+                for assoc in outdata.creating_job_associations:
+                    job = assoc.job
+                    break   
+                if job:
+                    assoc = self.app.model.JobToOutputDatasetAssociation( '__new_child_file_%s|%s__' % ( name, designation ), child_dataset )
+                    assoc.job = job
+                    assoc.flush()
+                child_dataset.state = outdata.state
                 child_dataset.flush()
                 # Add child to return dict 
                 children[name][designation] = child_dataset
@@ -1550,7 +1559,7 @@
def collect_primary_datasets( self, output):
         primary_datasets = {}
-        #Loop through output file names, looking for generated primary datasets in form of 'primary_associatedWithDatasetID_designation_visibility_extension'
+        #Loop through output file names, looking for generated primary datasets in form of 'primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY)'
         for name, outdata in output.items():
             for filename in glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ):
                 if not name in primary_datasets:
@@ -1563,19 +1572,32 @@
                 if visible == "visible": visible = True
                 else: visible = False
                 ext = fields.pop(0).lower()
+                dbkey = outdata.dbkey
+                if fields:
+                    dbkey = fields[ 0 ]
                 # Create new primary dataset
-                primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=outdata.dbkey, create_dataset=True )
+                primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=dbkey, create_dataset=True )
                 self.app.security_agent.copy_dataset_permissions( outdata.dataset, primary_data.dataset )
                 primary_data.flush()
                 # Move data from temp location to dataset location
                 shutil.move( filename, primary_data.file_name )
                 primary_data.set_size()
-                primary_data.name = dataset.name
-                primary_data.info = dataset.info
-                primary_data.state = primary_data.states.OK
-                primary_data.init_meta( copy_from=dataset )
+                primary_data.name = outdata.name
+                primary_data.info = outdata.info
+                primary_data.init_meta( copy_from=outdata )
+                primary_data.dbkey = dbkey
                 primary_data.set_meta()
                 primary_data.set_peek()
+                # Associate new dataset with job
+                job = None
+                for assoc in outdata.creating_job_associations:
+                    job = assoc.job
+                    break   
+                if job:
+                    assoc = self.app.model.JobToOutputDatasetAssociation( '__new_primary_file_%s|%s__' % ( name, designation ), primary_data )
+                    assoc.job = job
+                    assoc.flush()
+                primary_data.state = outdata.state
                 primary_data.flush()
                 outdata.history.add_dataset( primary_data )
                 # Add dataset to return dict 
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/tools/actions/upload.py
--- a/lib/galaxy/tools/actions/upload.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/tools/actions/upload.py	Sat Aug 22 23:20:09 2009 -0400
@@ -20,12 +20,10 @@
             for upload_dataset in incoming['files']:
                 f = upload_dataset['file_data']
                 if isinstance( f, FieldStorage ): 
-                    # very small files can be StringIOs
-                    if 'name' in dir( f.file ) and f.file.name != '<fdopen>':
-                        local_filename = util.mkstemp_ln( f.file.name, 'upload_file_data_' )
-                        f.file.close()
-                    else:
-                        local_filename = datatypes.sniff.stream_to_file( f.file, prefix="strio_upload_file_" )[0]
+                    assert not isinstance( f.file, StringIO.StringIO )
+                    assert f.file.name != '<fdopen>'
+                    local_filename = util.mkstemp_ln( f.file.name, 'upload_file_data_' )
+                    f.file.close()
                     upload_dataset['file_data'] = dict( filename = f.filename,
                                                         local_filename = local_filename )
                 if upload_dataset['url_paste'].strip() != '':
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/tools/parameters/dynamic_options.py
--- a/lib/galaxy/tools/parameters/dynamic_options.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/tools/parameters/dynamic_options.py	Sat Aug 22 23:20:09 2009 -0400
@@ -242,6 +242,55 @@
             rval.append( add_value )
         return rval
+class RemoveValueFilter( Filter ):
+    """
+    Removes a value from an options list.
+    
+    Type: remove_value
+    
+    Required Attributes:
+        value: value to remove from select list
+            or
+        ref: param to refer to
+            or
+        meta_ref: dataset to refer to
+        key: metadata key to compare to
+    """
+    def __init__( self, d_option, elem ):
+        Filter.__init__( self, d_option, elem )
+        self.value = elem.get( "value", None )
+        self.ref_name = elem.get( "ref", None )
+        self.meta_ref = elem.get( "meta_ref", None )
+        self.metadata_key = elem.get( "key", None )
+        assert self.value is not None or ( ( self.ref_name is not None or self.meta_ref is not None )and self.metadata_key is not None ), ValueError( "Required 'value' or 'ref' and 'key' attributes missing from filter" )
+        self.multiple = string_as_bool( elem.get( "multiple", "False" ) )
+        self.separator = elem.get( "separator", "," )
+    def filter_options( self, options, trans, other_values ):
+        if trans is not None and trans.workflow_building_mode: return options
+        assert self.value is not None or ( self.ref_name is not None and self.ref_name in other_values ) or (self.meta_ref is not None and self.meta_ref in other_values ) or ( trans is not None and trans.workflow_building_mode), Exception( "Required dependency '%s' or '%s' not found in incoming values" % ( self.ref_name, self.meta_ref ) )
+        def compare_value( option_value, filter_value ):
+            if isinstance( filter_value, list ):
+                if self.multiple:
+                    option_value = option_value.split( self.separator )
+                    for value in filter_value:
+                        if value not in filter_value:
+                            return False
+                    return True
+                return option_value in filter_value
+            if self.multiple:
+                return filter_value in option_value.split( self.separator )
+            return option_value == filter_value
+        value = self.value
+        if value is None:
+            if self.ref_name is not None:
+                value = other_values.get( self.ref_name )
+            else:
+                data_ref = other_values.get( self.meta_ref )
+                if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ):
+                    return options #cannot modify options
+                value = data_ref.metadata.get( self.metadata_key, None )
+        return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ]
+
 class SortByColumnFilter( Filter ):
     """
     Sorts an options list by a column
@@ -274,6 +323,7 @@
                      unique_value = UniqueValueFilter,
                      multiple_splitter = MultipleSplitterFilter,
                      add_value = AdditionalValueFilter,
+                     remove_value = RemoveValueFilter,
                      sort_by = SortByColumnFilter )
class DynamicOptions( object ):
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/web/controllers/admin.py	Sat Aug 22 23:20:09 2009 -0400
@@ -764,11 +764,7 @@
                 # See if we have any field contents
                 info = info_association.info
                 if info:
-                    field_contents = {}
-                    for index, value in enumerate( info.content ):
-                        key = 'field_%i' % index
-                        field_contents[ key ] = value
-                    widgets = get_form_widgets( trans, template, field_contents )
+                    widgets = get_form_widgets( trans, template, info.content )
                 else:
                     widgets = get_form_widgets( trans, template )
             else:
@@ -965,11 +961,7 @@
                 # See if we have any field contents
                 info = info_association.info
                 if info:
-                    field_contents = {}
-                    for index, value in enumerate( info.content ):
-                        key = 'field_%i' % index
-                        field_contents[ key ] = value
-                    widgets = get_form_widgets( trans, template, field_contents )
+                    widgets = get_form_widgets( trans, template, info.content )
                 else:
                     widgets = get_form_widgets( trans, template )
             else:
@@ -1220,11 +1212,7 @@
                 # See if we have any field contents
                 info = info_association.info
                 if info:
-                    field_contents = {}
-                    for index, value in enumerate( info.content ):
-                        key = 'field_%i' % index
-                        field_contents[ key ] = value
-                    widgets = get_form_widgets( trans, template, field_contents )
+                    widgets = get_form_widgets( trans, template, info.content )
                 else:
                     widgets = get_form_widgets( trans, template )
             else:
@@ -2027,7 +2015,7 @@
         num_states = int( util.restore_text( params.get( 'num_states', 0 ) ))
         proceed = True
         for i in range( num_states ):
-            if not util.restore_text( params.get( 'new_element_name_%i' % i, None ) ):
+            if not util.restore_text( params.get( 'state_name_%i' % i, None ) ):
                 proceed = False
                 break
         if not proceed:
@@ -2045,8 +2033,8 @@
             ss.delete()
             ss.flush()
         for i in range( num_states ):
-            name = util.restore_text( params.get( 'new_element_name_%i' % i, None ))
-            desc = util.restore_text( params.get( 'new_element_description_%i' % i, None ))
+            name = util.restore_text( params.get( 'state_name_%i' % i, None ))
+            desc = util.restore_text( params.get( 'state_desc_%i' % i, None ))
             ss = trans.app.model.SampleState(name, desc, rt) 
             ss.flush()
         msg = "The new request type named '%s' with %s state(s) has been created" % (rt.name, num_states)
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/forms.py
--- a/lib/galaxy/web/controllers/forms.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/web/controllers/forms.py	Sat Aug 22 23:20:09 2009 -0400
@@ -175,7 +175,7 @@
                         'visible': True,
                         'required': False,
                         'type': BaseField.form_field_types()[0],
-                        'selectlist': '' }
+                        'selectlist': [] }
         self.current_form['fields'].append(empty_field)
     def __get_field(self, index, **kwd):
         params = util.Params( kwd )
@@ -183,10 +183,10 @@
         # 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, None ) )
-        helptext = util.restore_text( params.get( 'field_helptext_%i' % index, None ) )
+        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 )
-        field_type = util.restore_text( params.get( 'field_type_%i' % index, None ) )
+        field_type = util.restore_text( params.get( 'field_type_%i' % index, '' ) )
         if field_type == 'SelectField':
             selectlist = self.__get_selectbox_options(index, **kwd)
             return {'label': name, 
@@ -419,22 +419,39 @@
     else:
         fdc_list = trans.app.model.FormDefinitionCurrent.query().all()
     return [ fdc.latest_form for fdc in fdc_list ]
-def get_form_widgets( trans, form, contents={} ):
+
+
+def get_form_widgets( trans, form, contents=[], user=None, **kwd ):
     '''
     Return the list of widgets that comprise a form definition,
     including field contents if any.
     '''
+    params = util.Params( kwd )
+    if not user:
+        user = trans.user
     widgets = []
     for index, field in enumerate( form.fields ):
         field_name = 'field_%i' % index
-        if field_name in contents:
-            value = contents[ field_name ]
-        elif field[ 'type' ] == 'CheckboxField':
-            # Since we do not have contents, set checkbox value to False
-            value = False
+        # determine the value of the field
+        if field_name in kwd:
+            # the user had already filled out this field and the same form is re-rendered 
+            # due to some reason like required fields have been left out.
+            if field[ 'type' ] == 'CheckboxField':
+                value = CheckboxField.is_checked( util.restore_text( params.get( field_name, False ) ) )
+            else:
+                value = util.restore_text( params.get( field_name, ''  ) )
+        elif contents:
+            # this field has a saved value
+            value = str(contents[ index ])
         else:
-            # Set other field types to empty string
-            value = ''
+            # if none of the above, then leave the field empty
+            if field[ 'type' ] == 'CheckboxField':
+                # Since we do not have contents, set checkbox value to False
+                value = False
+            else:
+                # Set other field types to empty string
+                value = ''
+        # create the field widget
         field_widget = eval( field[ 'type' ] )( field_name )
         if field[ 'type' ] == 'TextField':
             field_widget.set_size( 40 )
@@ -442,6 +459,10 @@
         elif field[ 'type' ] == 'TextArea':
             field_widget.set_size( 3, 40 )
             field_widget.value = value
+        elif field['type'] == 'AddressField':
+            field_widget.user = user
+            field_widget.value = value
+            field_widget.params = params
         elif field[ 'type' ] == 'SelectField':
             for option in field[ 'selectlist' ]:
                 if option == value:
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/library.py
--- a/lib/galaxy/web/controllers/library.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/web/controllers/library.py	Sat Aug 22 23:20:09 2009 -0400
@@ -137,11 +137,7 @@
                 # See if we have any field contents
                 info = library.info_association[0].info
                 if info:
-                    field_contents = {}
-                    for index, value in enumerate( info.content ):
-                        key = 'field_%i' % index
-                        field_contents[ key ] = value
-                    widgets = get_form_widgets( trans, template, field_contents )
+                    widgets = get_form_widgets( trans, template, info.content )
                 else:
                     widgets = get_form_widgets( trans, template )
             else:
@@ -475,11 +471,7 @@
                 # See if we have any field contents
                 info = info_association.info
                 if info:
-                    field_contents = {}
-                    for index, value in enumerate( info.content ):
-                        key = 'field_%i' % index
-                        field_contents[ key ] = value
-                    widgets = get_form_widgets( trans, template, field_contents )
+                    widgets = get_form_widgets( trans, template, info.content )
                 else:
                     widgets = get_form_widgets( trans, template )
             else:
@@ -996,11 +988,7 @@
                 # See if we have any field contents
                 info = info_association.info
                 if info:
-                    field_contents = {}
-                    for index, value in enumerate( info.content ):
-                        key = 'field_%i' % index
-                        field_contents[ key ] = value
-                    widgets = get_form_widgets( trans, template, field_contents )
+                    widgets = get_form_widgets( trans, template, info.content )
                 else:
                     widgets = get_form_widgets( trans, template )
             else:
@@ -1173,3 +1161,13 @@
                                                           edit_info=True,
                                                           msg=util.sanitize_text( msg ),
                                                           messagetype='done' ) )
+
+
+def get_authorized_libs(trans, user):
+    all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all()
+    authorized_libraries = []
+    for library in all_libraries:
+        if trans.app.security_agent.allow_action(user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) \
+            or trans.app.security_agent.allow_action(user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library):
+            authorized_libraries.append(library)
+    return authorized_libraries
\ No newline at end of file
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/requests.py
--- a/lib/galaxy/web/controllers/requests.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/web/controllers/requests.py	Sat Aug 22 23:20:09 2009 -0400
@@ -8,6 +8,8 @@
 from galaxy.web.form_builder import * 
 from datetime import datetime, timedelta
 from cgi import escape, FieldStorage
+from galaxy.web.controllers.forms import get_form_widgets
+from galaxy.web.controllers.library import get_authorized_libs
log = logging.getLogger( __name__ )
@@ -62,18 +64,12 @@
     request_grid = RequestsListGrid()
@web.expose
+    @web.require_login( "create/submit sequencing requests" )
     def index( self, trans ):
         return trans.fill_template( "requests/index.mako" )
-    
-    def get_authorized_libs(self, trans):
-        all_libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all()
-        authorized_libraries = []
-        for library in all_libraries:
-            if trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library) \
-                or trans.app.security_agent.allow_action(trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library):
-                authorized_libraries.append(library)
-        return authorized_libraries
+
     @web.expose
+    @web.require_login( "create/submit sequencing requests" )
     def list( self, trans, **kwargs ):
         '''
         List all request made by the current user
@@ -137,7 +133,6 @@
         Shows the request details
         '''
         request = trans.app.model.Request.get(id)
-        libraries = self.get_authorized_libs(trans)
         # list of widgets to be rendered on the request form
         request_details = []
         # main details
@@ -146,6 +141,9 @@
                                     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, 
@@ -201,6 +199,7 @@
             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', ''  ) )
@@ -326,6 +325,7 @@
@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', ''  ) )
@@ -348,6 +348,7 @@
                                     edit_mode=self.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', ''  ) )
@@ -384,6 +385,7 @@
                     select_reqtype.add_option(rt.name, rt.id)
         return select_reqtype
     @web.expose
+    @web.require_login( "create/submit sequencing requests" )
     def new(self, trans, **kwd):
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
@@ -413,8 +415,8 @@
                 if params.get('create_request_button', False) == 'Save':
                     return trans.response.send_redirect( web.url_for( controller='requests',
                                                                       action='list',
-                                                                      msg=msg ,
-                                                                      messagetype='done') )
+                                                                      message=msg ,
+                                                                      status='done') )
                 elif params.get('create_request_samples_button', False) == 'Add samples':
                     new_kwd = {}
                     new_kwd['id'] = trans.security.encode_id(request.id)
@@ -457,12 +459,10 @@
                             helptext='(Optional)'))
# libraries selectbox
-        libraries = self.get_authorized_libs(trans)
+        libraries = get_authorized_libs(trans, trans.user)
         libui = self.__library_ui(libraries, **kwd)
         widgets = widgets + libui
-        widgets = self.__create_form(trans, request_type.request_form_id, widgets, 
-                                     form_values, **kwd)
-        title = 'Add a new request of type: %s' % request_type.name
+        widgets = widgets + get_form_widgets(trans, request_type.request_form, contents=[], **kwd)
         return trans.fill_template( '/requests/new_request.mako',
                                     select_request_type=select_request_type,
                                     request_type=request_type,                                    
@@ -502,58 +502,13 @@
             return [widget, new_lib]
         else:
             return [widget]
-        
-    def __create_form(self, trans, form_id, widgets=[], form_values=None, **kwd):
-        # TODO: RC - replace this method by importing as follows:
-        # from galaxy.web.controllers.forms import get_form_widgets
-        params = util.Params( kwd )
-        form = trans.app.model.FormDefinition.get(form_id)
-        # form fields
-        for index, field in enumerate(form.fields):
-            # value of the field 
-            if field['type'] == 'CheckboxField':
-                value = util.restore_text( params.get( 'field_%i' % index, False  ) )
-            else:
-                value = util.restore_text( params.get( 'field_%i' % index, ''  ) )
-            if not value:
-                if form_values:
-                    value = str(form_values.content[index])
-            # create the field
-            fw = eval(field['type'])('field_%i' % index)
-            if field['type'] == 'TextField':
-                fw.set_size(40)
-                fw.value = value
-            elif field['type'] == 'TextArea':
-                fw.set_size(3, 40)
-                fw.value = value
-            elif field['type'] == 'AddressField':
-                fw.user = trans.user
-                fw.value = value
-                fw.params = params
-            elif field['type'] == 'SelectField':
-                for option in field['selectlist']:
-                    if option == value:
-                        fw.add_option(option, option, selected=True)
-                    else:
-                        fw.add_option(option, option)
-            elif field['type'] == 'CheckboxField':
-                fw.checked = value
-            # require/optional
-            if field['required'] == 'required':
-                req = 'Required'
-            else:
-                req = 'Optional'
-            widgets.append(dict(label=field['label'],
-                                widget=fw,
-                                helptext=field['helptext']+' ('+req+')'))
-        return widgets
     def __validate(self, trans, request):
         '''
         Validates the request entered by the user 
         '''
         empty_fields = []
-        if not request.library:
-            empty_fields.append('Data library')
+#        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]:
@@ -622,6 +577,7 @@
             request.flush()
         return request
     @web.expose
+    @web.require_login( "create/submit sequencing requests" )
     def edit(self, trans, **kwd):
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
@@ -698,11 +654,10 @@
                             helptext='(Optional)'))
# libraries selectbox
-        libraries = self.get_authorized_libs(trans)
+        libraries = get_authorized_libs(trans, trans.user)
         libui = self.__library_ui(libraries, request, **kwd)
         widgets = widgets + libui
-        widgets = self.__create_form(trans, request.type.request_form_id, widgets, 
-                                     request.values, **kwd)
+        widgets = widgets + get_form_widgets(trans, request.type.request_form, request.values.content, **kwd)
         return trans.fill_template( '/requests/edit_request.mako',
                                     select_request_type=select_request_type,
                                     request_type=request.type,
@@ -735,6 +690,8 @@
         kwd['id'] = trans.security.encode_id(request.id)
         return trans.response.send_redirect( web.url_for( controller='requests',
                                                           action='list',
+                                                          status='done',
+                                                          message='The request <b>%s</b> has been deleted.' % request.name,                                                          
                                                           **kwd) )
     def __undelete_request(self, trans, id):
         try:
@@ -754,6 +711,8 @@
         kwd['id'] = trans.security.encode_id(request.id)
         return trans.response.send_redirect( web.url_for( controller='requests',
                                                           action='list',
+                                                          status='done',
+                                                          message='The request <b>%s</b> has been undeleted.' % request.name,                                                          
                                                           **kwd) )
     def __submit(self, trans, id):
         try:
@@ -784,10 +743,14 @@
         request.flush()
         kwd = {}
         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',
                                                           action='list',
+                                                          show_filter=trans.app.model.Request.states.SUBMITTED,
                                                           **kwd) )
     @web.expose
+    @web.require_login( "create/submit sequencing requests" )
     def submit_request(self, trans, **kwd):
         params = util.Params( kwd )
         try:
@@ -817,13 +780,16 @@
         # change request's submitted field
         request.state = request.states.SUBMITTED
         request.flush()
-        ## TODO
         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',
                                                           action='list',
+                                                          show_filter=trans.app.model.Request.states.SUBMITTED,
                                                           **kwd) )
@web.expose
+    @web.require_login( "create/submit sequencing requests" )
     def show_events(self, trans, **kwd):
         params = util.Params( kwd )
         try:
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/requests_admin.py
--- a/lib/galaxy/web/controllers/requests_admin.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/web/controllers/requests_admin.py	Sat Aug 22 23:20:09 2009 -0400
@@ -7,19 +7,20 @@
 import logging, tempfile, zipfile, tarfile, os, sys
 from galaxy.web.form_builder import * 
 from datetime import datetime, timedelta
+from galaxy.web.controllers.forms import get_form_widgets
+from galaxy.web.controllers.library import get_authorized_libs
log = logging.getLogger( __name__ )
-
-# States for passing messages
-SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
class RequestsListGrid( grids.Grid ):
     title = "Sequencing Requests"
     model_class = model.Request
     default_sort_key = "-create_time"
+    show_filter = model.Request.states.SUBMITTED
     columns = [
         grids.GridColumn( "Name", key="name",
-                          link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) )),
+                          link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ),
+                          attach_popup=True ),
         grids.GridColumn( "Description", key="desc"),
         grids.GridColumn( "Sample(s)", method='number_of_samples',
                           link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ),
@@ -30,15 +31,18 @@
]
     operations = [
-#        grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted )  ),
-#        grids.GridOperation( "Samples", allow_multiple=False, condition=( lambda item: not item.deleted )  ),
-#        grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ),
-#        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),    
+        grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() and item.samples )  ),
+        grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted )  ),
+        grids.GridOperation( "Delete", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() )  ),
+        grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),    
     ]
     standard_filters = [
+        grids.GridColumnFilter( model.Request.states.UNSUBMITTED, 
+                                args=dict( state=model.Request.states.UNSUBMITTED, deleted=False ) ),
         grids.GridColumnFilter( model.Request.states.SUBMITTED, 
                                 args=dict( state=model.Request.states.SUBMITTED, deleted=False ) ),
         grids.GridColumnFilter( model.Request.states.COMPLETE, args=dict( state=model.Request.states.COMPLETE, deleted=False ) ),
+        grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
         grids.GridColumnFilter( "All", args=dict( deleted=False ) )
     ]
     def get_user(self, trans, request):
@@ -48,9 +52,9 @@
     def get_request_type(self, trans, request):
         request_type = trans.app.model.RequestType.get(request.request_type_id)
         return request_type.name
-    def apply_default_filter( self, trans, query ):
-        return query.filter(or_(self.model_class.state==self.model_class.states.SUBMITTED, 
-                                self.model_class.state==self.model_class.states.COMPLETE))
+#    def apply_default_filter( self, trans, query ):
+#        return query.filter(or_(self.model_class.state==self.model_class.states.SUBMITTED, 
+#                                self.model_class.state==self.model_class.states.COMPLETE))
     def number_of_samples(self, trans, request):
         return str(len(request.samples))
@@ -67,32 +71,277 @@
         '''
         List all request made by the current user
         '''
-        status = message = None
+        message = util.restore_text( kwargs.get( 'message', ''  ) )
+        status = kwargs.get( 'status', 'done' )
         self.request_grid.default_filter = dict(state=trans.app.model.Request.states.SUBMITTED, 
                                                 deleted=False)
         if 'operation' in kwargs:
             operation = kwargs['operation'].lower()
             if operation == "show_request":
                 id = trans.security.decode_id(kwargs['id'])
-                return self.__show_request(trans, id)
-
+                return self.__show_request(trans, id, status, message)
+            elif operation == "submit":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.__submit(trans, id)
+            elif operation == "edit":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.__edit_request(trans, id)
+            elif operation == "delete":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.__delete_request(trans, id)
+            elif operation == "undelete":
+                id = trans.security.decode_id(kwargs['id'])
+                return self.__undelete_request(trans, id)
         if 'show_filter' in kwargs.keys():
             if kwargs['show_filter'] == 'All':
-                self.request_grid.default_filter = dict(deleted=False)
+                self.request_grid.default_filter = {}
+            elif kwargs['show_filter'] == 'Deleted':
+                self.request_grid.default_filter = dict(deleted=True)
             else:
-                self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False)
+                self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False)   
+        self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED)
         # Render the list view
         return self.request_grid( trans, template='/admin/requests/grid.mako', **kwargs )
-    def __show_request(self, trans, id):
+    @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)
+    def __edit_request(self, trans, id, **kwd):
         try:
             request = trans.app.model.Request.get(id)
         except:
-            return trans.response.send_redirect( web.url_for( controller='requests',
+            msg = "Invalid request ID"
+            log.warn( msg )
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              status='error',
+                                                              message=msg) )
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        select_request_type = self.__select_request_type(trans, request.type.id)
+        # list of widgets to be rendered on the request form
+        widgets = []
+        if util.restore_text( params.get( 'name', ''  ) ):
+            name = util.restore_text( params.get( 'name', ''  ) )
+        else:
+            name = request.name
+        widgets.append(dict(label='Name', 
+                            widget=TextField('name', 40, name), 
+                            helptext='(Required)'))
+        if util.restore_text( params.get( 'desc', ''  ) ):
+            desc = util.restore_text( params.get( 'desc', ''  ) )
+        else:
+            desc = request.desc
+        widgets.append(dict(label='Description', 
+                            widget=TextField('desc', 40, desc), 
+                            helptext='(Optional)'))
+        # libraries selectbox
+        libui = self.__library_ui(trans, request.user, request, **kwd)
+        widgets = widgets + libui
+        widgets = widgets + get_form_widgets(trans, request.type.request_form, request.values.content, request.user, **kwd)
+        return trans.fill_template( '/admin/requests/edit_request.mako',
+                                    select_request_type=select_request_type,
+                                    request_type=request.type,
+                                    request=request,
+                                    widgets=widgets,
+                                    msg=msg,
+                                    messagetype=messagetype)
+        return self.__show_request_form(trans)
+    def __delete_request(self, trans, id):
+        try:
+            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) )
+        # change request's submitted field
+        if not request.unsubmitted():
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              status='error',
+                                                              message='This request cannot be deleted as it is already been submitted',
+                                                              **kwd) )
+        request.deleted = True
+        request.flush()
+        kwd = {}
+        kwd['id'] = trans.security.encode_id(request.id)
+        return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                          action='list',
+                                                          show_filter=trans.app.model.Request.states.UNSUBMITTED,
+                                                          status='done',
+                                                          message='The request <b>%s</b> has been deleted.' % request.name,
+                                                          **kwd) )
+    def __undelete_request(self, trans, id):
+        try:
+            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) )
+        # change request's submitted field
+        request.deleted = False
+        request.flush()
+        kwd = {}
+        kwd['id'] = trans.security.encode_id(request.id)
+        return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                          action='list',
+                                                          show_filter=trans.app.model.Request.states.UNSUBMITTED,
+                                                          status='done',
+                                                          message='The request <b>%s</b> has been undeleted.' % request.name,                                                          
+                                                          **kwd) )
+    def __submit(self, trans, id):
+        try:
+            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 = {}
+        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) )
+    @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'
@@ -100,8 +349,163 @@
                                     request=request,
                                     request_details=self.request_details(trans, id),
                                     current_samples = self.current_samples, 
-                                    details_state=self.details_state)
+                                    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', ''  ) )
@@ -128,24 +532,28 @@
         # 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=''))
-        request_details.append(dict(label='Date updated', 
-                                    value=request.create_time, 
-                                    helptext=''))
-        request_details.append(dict(label='User', 
-                                    value=str(request.user.email), 
-                                    helptext=''))
         # library associated
+        if request.library:
+			value=request.library.name
+        else:
+			value = None
         request_details.append(dict(label='Data library', 
-                            value=trans.app.model.Library.get(request.library_id).name, 
+                            value=value, 
                             helptext='Data library where the resultant dataset will be stored'))
         # form fields
         for index, field in enumerate(request.type.request_form.fields):
@@ -167,15 +575,262 @@
                                             value=request.values.content[index],
                                             helptext=field['helptext']+' ('+req+')'))
         return request_details
+    
+    def __select_request_type(self, trans, rtid):
+        rt_ids = ['none']
+        for rt in trans.app.model.RequestType.query().all():
+            if not rt.deleted:
+                rt_ids.append(str(rt.id))
+        select_reqtype = SelectField('select_request_type', 
+                                     refresh_on_change=True, 
+                                     refresh_on_change_values=rt_ids[1:])
+        if rtid == 'none':
+            select_reqtype.add_option('Select one', 'none', selected=True)
+        else:
+            select_reqtype.add_option('Select one', 'none')
+        for rt in trans.app.model.RequestType.query().all():
+            if not rt.deleted:
+                if rtid == rt.id:
+                    select_reqtype.add_option(rt.name, rt.id, selected=True)
+                else:
+                    select_reqtype.add_option(rt.name, rt.id)
+        return select_reqtype
+    @web.expose
+    @web.require_admin
+    def new(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        if params.get('select_request_type', False) == 'True':
+            return trans.fill_template( '/admin/requests/new_request.mako',
+                                        select_request_type=self.__select_request_type(trans, 'none'),                                 
+                                        widgets=[],                                   
+                                        msg=msg,
+                                        messagetype=messagetype)
+        elif params.get('create', False) == 'True':
+            if params.get('create_request_button', False) == 'Save' \
+               or params.get('create_request_samples_button', False) == 'Add samples':
+                request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+                if not util.restore_text(params.get('name', '')) \
+                    or util.restore_text(params.get('select_user', '')) == unicode('none'):
+                    msg = 'Please enter the <b>Name</b> of the request and the <b>user</b> on behalf of whom this request will be submitted before saving this request'
+                    kwd['create'] = 'True'
+                    kwd['messagetype'] = 'error'
+                    kwd['msg'] = msg
+                    kwd['create_request_button'] = None
+                    kwd['create_request_samples_button'] = None
+                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                                      action='new',
+                                                                      **kwd) )
+                request = self.__save_request(trans, None, **kwd)
+                msg = 'The new request named %s has been created' % request.name
+                if params.get('create_request_button', False) == 'Save':
+                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                                      action='list',
+                                                                      show_filter=trans.app.model.Request.states.UNSUBMITTED,
+                                                                      message=msg ,
+                                                                      status='done') )
+                elif params.get('create_request_samples_button', False) == 'Add samples':
+                    new_kwd = {}
+                    new_kwd['id'] = trans.security.encode_id(request.id)
+                    new_kwd['operation'] = 'show_request'
+                    new_kwd['add_sample'] = True
+                    return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                                      action='list',
+                                                                      message=msg ,
+                                                                      status='done',
+                                                                      **new_kwd) )
+            else:
+                return self.__show_request_form(trans, **kwd)
+        elif params.get('refresh', False) == 'true':
+            return self.__show_request_form(trans, **kwd)
+    def __show_request_form(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        try:
+            request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+        except:
+            return trans.fill_template( '/admin/requests/new_request.mako',
+                                        select_request_type=self.__select_request_type(trans, 'none'),                                 
+                                        widgets=[],                                   
+                                        msg=msg,
+                                        messagetype=messagetype)
+        form_values = None
+        select_request_type = self.__select_request_type(trans, request_type.id)
+        # user
+        user_id = params.get( 'select_user', 'none' )
+        try:
+            user = trans.app.model.User.get(int(user_id))
+        except:
+            user = None
+        # list of widgets to be rendered on the request form
+        widgets = []
+        widgets.append(dict(label='Select user',
+                            widget=self.__select_user(trans, user_id),
+                            helptext='The request would be submitted on behalf of this user (Required)'))
+        widgets.append(dict(label='Name', 
+                            widget=TextField('name', 40, 
+                                             util.restore_text( params.get( 'name', ''  ) )), 
+                            helptext='(Required)'))
+        widgets.append(dict(label='Description', 
+                            widget=TextField('desc', 40,
+                                             util.restore_text( params.get( 'desc', ''  ) )), 
+                            helptext='(Optional)'))
+        # libraries selectbox
+        libui = self.__library_ui(trans, user, **kwd)
+        widgets = widgets + libui
+        widgets = widgets + get_form_widgets(trans, request_type.request_form, contents=[], user=user, **kwd)
+        return trans.fill_template( '/admin/requests/new_request.mako',
+                                    select_request_type=select_request_type,
+                                    request_type=request_type,                                    
+                                    widgets=widgets,
+                                    msg=msg,
+                                    messagetype=messagetype)
+    def __select_user(self, trans, userid):
+        user_ids = ['none']
+        for user in trans.app.model.User.query().all():
+            if not user.deleted:
+                user_ids.append(str(user.id))
+        select_user = SelectField('select_user', 
+                                  refresh_on_change=True, 
+                                  refresh_on_change_values=user_ids[1:])
+        if userid == 'none':
+            select_user.add_option('Select one', 'none', selected=True)
+        else:
+            select_user.add_option('Select one', 'none')
+        for user in trans.app.model.User.query().all():
+            if not user.deleted:
+                if userid == str(user.id):
+                    select_user.add_option(user.email, user.id, selected=True)
+                else:
+                    select_user.add_option(user.email, user.id)
+        return select_user
+        
+    def __library_ui(self, trans, user, request=None, **kwd):
+        params = util.Params( kwd )
+        lib_id = params.get( 'library_id', 'none'  )
+        if not user:
+            libraries = trans.app.model.Library.filter(trans.app.model.Library.table.c.deleted == False).order_by(trans.app.model.Library.name).all()
+        else:
+            libraries = get_authorized_libs(trans, user)
+        lib_list = SelectField('library_id', refresh_on_change=True, 
+                               refresh_on_change_values=['new'])
+        if request and lib_id == 'none':
+            if request.library:
+                lib_id = str(request.library.id)
+        if lib_id == 'none':
+            lib_list.add_option('Select one', 'none', selected=True)
+        else:
+            lib_list.add_option('Select one', 'none')
+        for lib in libraries:
+            if str(lib.id) == lib_id:
+                lib_list.add_option(lib.name, lib.id, selected=True)
+            else:
+                lib_list.add_option(lib.name, lib.id)
+        if lib_id == 'new':
+            lib_list.add_option('Create a new data library', 'new', selected=True)
+        else:
+            lib_list.add_option('Create a new data library', 'new')
+        widget = dict(label='Data library', 
+                      widget=lib_list, 
+                      helptext='Data library where the resultant dataset will be stored.')
+        if lib_id == 'new':
+            new_lib = dict(label='Create a new Library', 
+                           widget=TextField('new_library_name', 40,
+                                     util.restore_text( params.get( 'new_library_name', ''  ) )), 
+                           helptext='Enter a library name here to request a new library')
+            return [widget, new_lib]
+        else:
+            return [widget]
+    def __validate(self, trans, request):
+        '''
+        Validates the request entered by the user 
+        '''
+        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]:
+                empty_fields.append(field['label'])
+        if empty_fields:
+            msg = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name
+            for ef in empty_fields:
+                msg = msg + '<b>' +ef + '</b><br/>'
+            return msg
+        return None
+    def __save_request(self, trans, request=None, **kwd):
+        '''
+        This method saves a new request if request_id is None. 
+        '''
+        params = util.Params( kwd )
+        request_type = trans.app.model.RequestType.get(int(params.select_request_type))
+        if request:
+            user = request.user
+        else:
+            user = trans.app.model.User.get(int(params.get('select_user', '')))
+        name = util.restore_text(params.get('name', ''))
+        desc = util.restore_text(params.get('desc', ''))
+        # library
+        try:
+            library = trans.app.model.Library.get(int(params.get('library_id', None)))
+        except:
+            library = None
+        # fields
+        values = []
+        for index, field in enumerate(request_type.request_form.fields):
+            if field['type'] == 'AddressField':
+                value = util.restore_text(params.get('field_%i' % index, ''))
+                if value == 'new':
+                    # save this new address in the list of this user's addresses
+                    user_address = trans.app.model.UserAddress( user=user )
+                    user_address.desc = util.restore_text(params.get('field_%i_short_desc' % index, ''))
+                    user_address.name = util.restore_text(params.get('field_%i_name' % index, ''))
+                    user_address.institution = util.restore_text(params.get('field_%i_institution' % index, ''))
+                    user_address.address = util.restore_text(params.get('field_%i_address1' % index, ''))+' '+util.restore_text(params.get('field_%i_address2' % index, ''))
+                    user_address.city = util.restore_text(params.get('field_%i_city' % index, ''))
+                    user_address.state = util.restore_text(params.get('field_%i_state' % index, ''))
+                    user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, ''))
+                    user_address.country = util.restore_text(params.get('field_%i_country' % index, ''))
+                    user_address.phone = util.restore_text(params.get('field_%i_phone' % index, ''))
+                    user_address.flush()
+                    trans.user.refresh()
+                    values.append(int(user_address.id))
+                elif value == unicode('none'):
+                    values.append('')
+                else:
+                    values.append(int(value))
+            else:
+                values.append(util.restore_text(params.get('field_%i' % index, '')))
+        form_values = trans.app.model.FormValues(request_type.request_form, values)
+        form_values.flush()
+        if not request:
+            request = trans.app.model.Request(name, desc, request_type, 
+                                              user, form_values,
+                                              library=library, 
+                                              state=trans.app.model.Request.states.UNSUBMITTED)
+            request.flush()
+        else:
+            request.name = name
+            request.desc = desc
+            request.type = request_type
+            request.user = user
+            request.values = form_values
+            request.library = library
+            request.flush()
+        return request
     @web.expose
     @web.require_admin
     def bar_codes(self, trans, **kwd):
         params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
         request_id = params.get( 'request_id', None )
         if request_id:
             request = trans.app.model.Request.get( int( request_id ))
         if not request:
-            return trans.response.send_redirect( web.url_for( controller='requests',
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                               action='list',
                                                               status='error',
                                                               message="Invalid request ID",
@@ -191,7 +846,9 @@
                                      bc))
         return trans.fill_template( '/admin/samples/bar_codes.mako', 
                                     samples_list=[s for s in request.samples],
-                                    user=request.user, request=request, widgets=widgets)
+                                    user=request.user, request=request, widgets=widgets, 
+                                    messagetype=messagetype,
+                                    msg=msg)
     @web.expose
     @web.require_admin
     def save_bar_codes(self, trans, **kwd):
@@ -199,7 +856,7 @@
         try:
             request = trans.app.model.Request.get(int(params.get('request_id', None)))
         except:
-            return trans.response.send_redirect( web.url_for( controller='requests',
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                               action='list',
                                                               status='error',
                                                               message="Invalid request ID",
@@ -255,9 +912,10 @@
             sample.bar_code = bar_code
             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)) )
+                                                          action='bar_codes',
+                                                          request_id=request.id,
+                                                          msg='Bar codes has been saved for this request',
+                                                          messagetype='done'))
     def __set_request_state(self, request):
         # check if all the samples of the current request are in the final state
         complete = True 
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/tool_runner.py
--- a/lib/galaxy/web/controllers/tool_runner.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/web/controllers/tool_runner.py	Sat Aug 22 23:20:09 2009 -0400
@@ -82,7 +82,7 @@
             job = assoc.job
             break   
         if not job:
-            raise Exception("Failed to get job information for dataset hid %d" % hid)
+            raise Exception("Failed to get job information for dataset hid %d" % data.hid)
         # Get the tool object
         tool_id = job.tool_id
         try:
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/controllers/user.py
--- a/lib/galaxy/web/controllers/user.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/web/controllers/user.py	Sat Aug 22 23:20:09 2009 -0400
@@ -229,6 +229,8 @@
     def manage_addresses(self, trans, **kwd):
         if trans.user:
             params = util.Params( kwd )
+            msg = util.restore_text( params.get( 'msg', ''  ) )
+            messagetype = params.get( 'messagetype', 'done' )
             show_filter = util.restore_text( params.get( 'show_filter', 'Active'  ) )
             if show_filter == 'All':
                 addresses = [address for address in trans.user.addresses]
@@ -238,7 +240,9 @@
                 addresses = [address for address in trans.user.addresses if not address.deleted]
             return trans.fill_template( 'user/address.mako', 
                                         addresses=addresses,
-                                        show_filter=show_filter)
+                                        show_filter=show_filter,
+                                        msg=msg,
+                                        messagetype=messagetype)
         else:
             # User not logged in, history group must be only public
             return trans.show_error_message( "You must be logged in to change your default permitted actions." )
diff -r fbad627b45ac -r e6dda627e6b0 lib/galaxy/web/framework/base.py
--- a/lib/galaxy/web/framework/base.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/lib/galaxy/web/framework/base.py	Sat Aug 22 23:20:09 2009 -0400
@@ -216,11 +216,18 @@
 # tempfiles.  Necessary for externalizing the upload tool.  It's a little hacky
 # but for performance reasons it's way better to use Paste's tempfile than to
 # create a new one and copy.
-import cgi
+import cgi, tempfile
 class FieldStorage( cgi.FieldStorage ):
     def make_file(self, binary=None):
-        import tempfile
         return tempfile.NamedTemporaryFile()
+    def read_lines(self):
+    # Always make a new file
+        self.file = self.make_file()
+        self.__file = None
+        if self.outerboundary:
+            self.read_lines_to_outerboundary()
+        else:
+            self.read_lines_to_eof() 
 cgi.FieldStorage = FieldStorage
class Request( webob.Request ):
diff -r fbad627b45ac -r e6dda627e6b0 static/welcome.html
--- a/static/welcome.html	Sat Aug 22 23:18:47 2009 -0400
+++ b/static/welcome.html	Sat Aug 22 23:20:09 2009 -0400
@@ -71,7 +71,7 @@
         <table border="0" cellpadding="0" cellspacing="0" width="100%">
             <tr>
                 <td>
-                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:500,scroll:'no'})">
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/quickie1_TabSeq.flv',width:640,height:500,scroll:'no'})">
                       <div class="quickie">
                         <img src="images/qk/quickie1_small.png" border="0">
                       </div>
diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/forms/edit_form.mako
--- a/templates/admin/forms/edit_form.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/admin/forms/edit_form.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -70,7 +70,7 @@
 </%def>
<div class="toolForm">
-    <div class="toolFormTitle">Edit form definition '${form.name}'</div>
+    <div class="toolFormTitle">Edit form definition "${form.name}"</div>
     <form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id, num_fields=len(form.fields)  )}" method="post" >
         %for label, input in form_details:
             <div class="form-row">
diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/add_states.mako
--- a/templates/admin/requests/add_states.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/admin/requests/add_states.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -12,9 +12,9 @@
             %for element_count in range( num_states ):
                 <div class="form-row">
                     <label>${1+element_count}) State name:</label>
-                    <input type="text" name="new_element_name_${element_count}" value="" size="40"/>
+                    <input type="text" name="state_name_${element_count}" value="" size="40"/>
                     <label>State help text (optional):</label>
-                    <input type="text" name="new_element_description_${element_count}" value="" size="40"/>
+                    <input type="text" name="state_desc_${element_count}" value="" size="40"/>
                 </div>
                 <div style="clear: both"></div>
             %endfor
diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/edit_request.mako
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/admin/requests/edit_request.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -0,0 +1,88 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<script type="text/javascript">
+$( function() {
+    $( "select[refresh_on_change='true']").change( function() {
+        var refresh = false;
+        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+        if ( refresh_on_change_values ) {
+            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+            for( i= 0; i < refresh_on_change_values.length; i++ ) {
+                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+                    refresh = true;
+                    break;
+                }
+            }
+        }
+        else {
+            refresh = true;
+        }
+        if ( refresh ){
+            $( "#edit_request" ).submit();
+        }
+    });
+});
+</script>
+
+<br/>
+<br/>
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
+        <span>Browse this request</span></a>
+    </li>
+    <li>
+        <a class="action-button"  href="${h.url_for( controller='requests_admin', action='list')}">
+        <span>Browse requests</span></a>
+    </li>
+</ul>
+
+<div class="toolForm">
+    <div class="toolFormTitle">Edit request "${request.name}" from ${request.user.email}</div>
+    %if len(select_request_type.options) == 1:
+        There are no request types created for a new request.
+    %else:
+        <div class="toolFormBody">
+            <form name="edit_request" id="edit_request" action="${h.url_for( controller='requests_admin', action='edit', request_id=request.id)}" method="post" >
+                <div class="form-row">
+                    <label>
+                        Select Request Type:
+                    </label>
+                    ${select_request_type.get_html()}
+                </div>
+
+               %if select_request_type.get_selected() != ('Select one', 'none'):
+                   %for i, field in enumerate(widgets):
+                        <div class="form-row">
+                            <label>${field['label']}</label>
+                            ${field['widget'].get_html()}
+                            %if field['label'] == 'Library' and new_library:
+                                ${new_library.get_html()}
+                            %endif
+                            <div class="toolParamHelp" style="clear: both;">
+                                ${field['helptext']}
+                            </div>
+                            <div style="clear: both"></div>
+                        </div>
+                    %endfor                    
+                    <div class="form-row">
+                        <div style="float: left; width: 250px; margin-right: 10px;">
+                            <input type="hidden" name="refresh" value="true" size="40"/>
+                        </div>
+                      <div style="clear: both"></div>
+                    </div>
+                    <div class="form-row">
+                        <input type="submit" name="save_changes_request_button" value="Save changes"/> 
+                        ##<input type="submit" name="edit_samples_button" value="Edit samples"/>
+                    </div>
+               %endif
+        </form>
+    </div>
+</div>
+%endif
\ No newline at end of file
diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/grid.mako
--- a/templates/admin/requests/grid.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/admin/requests/grid.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -76,29 +76,28 @@
<div class="grid-header">
     <h2>${grid.title}</h2>
-    ##%if len(query.all()):
+    %if len(trans.app.model.Request.query().all()):
         ##<span class="title">Filter:</span>
         %for i, filter in enumerate( grid.standard_filters ):
             %if i > 0:    
                 <span>|</span>
             %endif
-            %if 'state' in grid.default_filter:
-                %if grid.default_filter['state'] == filter.label:
-                    <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span>
-                %else:
-                    <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span>
-                %endif
+            %if grid.show_filter == filter.label:
+                <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span>
             %else:
-                %if filter.label == 'All':
-                    <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}"><b>${filter.label}</b></a></span>
-                %else:
-                    <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span>
-                %endif
+                <span class="filter"><a href="${h.url_for( controller='requests_admin', action='list', show_filter=filter.label )}">${filter.label}</a></span>
             %endif
         %endfor
-    ##%endif
+    %endif
 </div>
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button" href="${h.url_for( controller='requests_admin', action='new', select_request_type=True )}">
+        <img src="${h.url_for('/static/images/silk/add.png')}" />
+        <span>Create a new request</span></a>
+    </li>
+</ul>
%if not len(query.all()):
     There are no requests.
diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/new_request.mako
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/admin/requests/new_request.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -0,0 +1,84 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<script type="text/javascript">
+$( function() {
+    $( "select[refresh_on_change='true']").change( function() {
+        var refresh = false;
+        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+        if ( refresh_on_change_values ) {
+            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+            for( i= 0; i < refresh_on_change_values.length; i++ ) {
+                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+                    refresh = true;
+                    break;
+                }
+            }
+        }
+        else {
+            refresh = true;
+        }
+        if ( refresh ){
+            $( "#new_request" ).submit();
+        }
+    });
+});
+</script>
+
+<br/>
+<br/>
+<ul class="manage-table-actions">
+    <li>
+        <a class="action-button"  href="${h.url_for( controller='requests_admin', action='list')}">
+        <span>Browse requests</span></a>
+    </li>
+</ul>
+
+<div class="toolForm">
+    <div class="toolFormTitle">Add a new request</div>
+    %if len(select_request_type.options) == 1:
+        There are no request types created for a new request.
+    %else:
+        <div class="toolFormBody">
+            <form name="new_request" id="new_request" action="${h.url_for( controller='requests_admin', action='new', create=True )}" method="post" >
+                <div class="form-row">
+                    <label>
+                        Select Request Type
+                    </label>
+                    ${select_request_type.get_html()}
+                </div>
+
+               %if select_request_type.get_selected() != ('Select one', 'none'):
+                   %for i, field in enumerate(widgets):
+                        <div class="form-row">
+                            <label>${field['label']}</label>
+                            ${field['widget'].get_html()}
+                            %if field['label'] == 'Library' and new_library:
+                                ${new_library.get_html()}
+                            %endif
+                            <div class="toolParamHelp" style="clear: both;">
+                                ${field['helptext']}
+                            </div>
+                            <div style="clear: both"></div>
+                        </div>
+                    %endfor                    
+                    <div class="form-row">
+                        <div style="float: left; width: 250px; margin-right: 10px;">
+                            <input type="hidden" name="refresh" value="true" size="40"/>
+                        </div>
+                      <div style="clear: both"></div>
+                    </div>
+                    <div class="form-row">
+                        <input type="submit" name="create_request_button" value="Save"/> 
+                        <input type="submit" name="create_request_samples_button" value="Add samples"/>
+                    </div>
+               %endif
+        </form>
+    </div>
+</div>
+%endif
\ No newline at end of file
diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/requests/show_request.mako
--- a/templates/admin/requests/show_request.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/admin/requests/show_request.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -12,18 +12,49 @@
 </div>
<ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}">
-        <span>Bar codes</span></a>
-    </li>
+    %if request.unsubmitted() and request.samples:
+        <li>
+            <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_admin', action='submit_request', id=request.id)}">
+            <span>Submit request</span></a>
+        </li>
+    %endif
+    %if request.submitted() and request.samples:
+        <li>
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}">
+            <span>Bar codes</span></a>
+        </li>
+    %endif
 </ul>
+
+<%def name="render_sample_form( index, sample_name, sample_values )">
+    <td>
+        <input type="text" name=sample_${index}_name value="${sample_name}" size="10"/>
+        <div class="toolParamHelp" style="clear: both;">
+            <i>${' (required)' }</i>
+        </div>
+    </td>
+    <td>
+    </td>
+    %for field_index, field in enumerate(request.type.sample_form.fields):
+        <td>
+            <input type="text" name=sample_${index}_field_${field_index} value="${sample_values[field_index]}" size="7"/>
+            <div class="toolParamHelp" style="clear: both;">
+                <i>${'('+field['required']+')' }</i>
+            </div>
+        </td>
+    %endfor   
+</%def>
<%def name="render_sample( index, sample )">
     <td>
         ${sample.name}
     </td>
     <td>
-        <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
+        %if sample.request.unsubmitted():
+            Unsubmitted
+        %else: 
+            <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
+        %endif
     </td>
     %for field_index, field in enumerate(request.type.sample_form.fields):
         <td>
@@ -34,10 +65,10 @@
             %endif
         </td>
     %endfor   
+
 </%def>
<div class="toolForm">
-    ##<div class="toolFormTitle">Request Details: '${request_details[0]['value']}'</div>
         <div class="form-row">
         <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id )}">${details_state}</a>
         </div>
@@ -57,13 +88,21 @@
                 </div>
                 <div style="clear: both"></div>
             %endfor
+            <div class="form-row">
+                <ul class="manage-table-actions">
+                    <li>
+                        <a class="action-button"  href="${h.url_for( controller='requests_admin', action='edit', show=True, request_id=request.id)}">
+                        <span>Edit request details</span></a>
+                    </li>
+                </ul>
+            </div>
         %endif
     </div>
 </div>
<div class="toolForm">
     ##<div class="toolFormTitle">Samples (${len(request.samples)})</div>
-    <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests', action='show_request', request_id=request.id )}" method="post" >
+    <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests_admin', action='show_request' )}" enctype="multipart/form-data" method="post" >
         <div class="form-row">
             %if current_samples: 
                 <table class="grid">
@@ -80,22 +119,88 @@
                                     </div>
                                 </th>
                             %endfor
+                            <th></th>
                         </tr>
                     <thead>
                     <tbody>
+                        <%
+                        request.refresh()
+                        %>
                         %for sample_index, sample in enumerate(current_samples):
-                            <tr>
-                                <td>${sample_index+1}</td>
-                                ${render_sample( sample_index, request.samples[sample_index] )}
-                            </tr>                            
+                            %if edit_mode:
+                                <tr>
+                                    <td>${sample_index+1}</td>
+                                    ${render_sample_form( sample_index, sample[0], sample[1])}
+                                </tr>      
+                            %else:
+                                <tr>
+                                    <td>${sample_index+1}</td>
+                                    %if sample_index in range(len(request.samples)):
+                                        ${render_sample( sample_index, request.samples[sample_index] )}
+                                    %else:                                                            
+                                        ${render_sample_form( sample_index, sample[0], sample[1])}
+                                    %endif
+                                    <td>
+                                        %if request.unsubmitted():
+                                            <a class="action-button" href="${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
+                                    </td>
+                                </tr>  
+                            %endif                            
                         %endfor
                     </tbody>
                 </table>
             %else:
                 <label>There are no samples.</label>
             %endif
-            
         </div>
-    ##</div>
+        %if not edit_mode:
+            <table class="grid">
+                <tbody>
+                    <tr>
+                        <div class="form-row">
+                            <td>
+                                %if current_samples and not request.complete():                        
+                                    <input type="submit" name="edit_samples_button" value="Edit samples"/>
+                                %endif
+                            </td>
+                            %if request.unsubmitted():
+                            <td>
+                                <label>Import from csv file</label>           
+                                <input type="file" name="file_data" />
+                                <input type="submit" name="import_samples_button" value="Import samples"/>
+                            </td>
+                            <td>
+                                %if current_samples:
+                                    <label>Copy from sample</label>
+                                    ${sample_copy.get_html()}
+                                %endif
+                                <input type="submit" name="add_sample_button" value="Add New"/>
+                            </td>
+                            %endif
+                        </div>
+                    </tr> 
+                </tbody>
+            </table>
+        %endif
+        %if request.samples or current_samples: 
+            <div class="form-row">
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="hidden" name="refresh" value="true" size="40"/>
+                </div>
+              <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                %if edit_mode:   
+                    <input type="submit" name="save_samples_button" value="Save"/>
+                    <input type="submit" name="cancel_changes_button" value="Cancel"/>
+                %elif request.unsubmitted():
+                    <input type="submit" name="save_samples_button" value="Save"/>
+                %endif
+            </div>
+        %endif
+        <input type="hidden" name="request_id" value="${request.id}" />
     </form>
 </div>
diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/samples/bar_codes.mako
--- a/templates/admin/samples/bar_codes.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/admin/samples/bar_codes.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -40,7 +40,7 @@
             </tbody>
         </table>
         <div class="form-row">
-            <input type="submit" name="save_new_sample_type" value="Save"/>
+            <input type="submit" name="save_bar_codes" value="Save"/>
         </div>
     </form>
 </div>
\ No newline at end of file
diff -r fbad627b45ac -r e6dda627e6b0 templates/admin/samples/events.mako
--- a/templates/admin/samples/events.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/admin/samples/events.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -56,7 +56,7 @@
                     </div>
                 %endfor
             <div class="form-row">
-                <input type="submit" name="add_event" value="Save"/>
+                <input type="submit" name="add_event_button" value="Save"/>
             </div>
         </form>
     </div>
diff -r fbad627b45ac -r e6dda627e6b0 templates/base_panels.mako
--- a/templates/base_panels.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/base_panels.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -138,7 +138,7 @@
${tab( "libraries", "Data Libraries", h.url_for( controller='library', action='index' ))}
-    %if trans.request_types():
+    %if trans.user and trans.request_types():
         <td class="tab">
             <a>Lab</a>
             <div class="submenu">
diff -r fbad627b45ac -r e6dda627e6b0 templates/requests/grid.mako
--- a/templates/requests/grid.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/requests/grid.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -76,7 +76,7 @@
<div class="grid-header">
     <h2>${grid.title}</h2>
-    ##%if len(query.all()):
+    %if len(trans.user.requests):
         ##<span class="title">Filter:</span>
         %for i, filter in enumerate( grid.standard_filters ):
             %if i > 0:    
@@ -88,17 +88,16 @@
                 <span class="filter"><a href="${h.url_for( controller='requests', action='list', show_filter=filter.label )}">${filter.label}</a></span>
             %endif
         %endfor
-    ##%endif
+    %endif
 </div>
<ul class="manage-table-actions">
     <li>
         <a class="action-button" href="${h.url_for( controller='requests', action='new', select_request_type=True )}">
         <img src="${h.url_for('/static/images/silk/add.png')}" />
-        <span>New request</span></a>
+        <span>Create a new request</span></a>
     </li>
 </ul>
-
%if not len(query.all()):
     There are no request(s).
@@ -215,4 +214,4 @@
         </tfoot>
     </table>
 </form>
-%endif
\ No newline at end of file
+%endif
diff -r fbad627b45ac -r e6dda627e6b0 templates/requests/show_request.mako
--- a/templates/requests/show_request.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/requests/show_request.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -68,7 +68,6 @@
 </%def>
<div class="toolForm">
-    ##<div class="toolFormTitle">Request Details: '${request_details[0]['value']}'</div>
         <div class="form-row">
         <a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id )}">${details_state}</a>
         </div>
@@ -217,7 +216,6 @@
                 %endif
             </div>
         %endif
-    ##</div>
-    <input type="hidden" name="request_id" value="${request.id}" />
+        <input type="hidden" name="request_id" value="${request.id}" />
     </form>
 </div>
diff -r fbad627b45ac -r e6dda627e6b0 templates/user/address.mako
--- a/templates/user/address.mako	Sat Aug 22 23:18:47 2009 -0400
+++ b/templates/user/address.mako	Sat Aug 22 23:20:09 2009 -0400
@@ -33,51 +33,48 @@
 </div>
-
-<div class="toolForm">
-    ##<div class="toolFormTitle">Addresses</div>
-    <div class="toolFormBody">
-        <% trans.user.refresh() %>
-        %if not trans.user.addresses:
-            <label>There are no addresses</label>
-        %else:
-            <table class="grid">
-                <tbody>
-                    %for index, address in enumerate(addresses):    
-                        <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
-                                         
-                            <td>
-                                <div class="form-row">   
-                                    <label>${address.desc}</label>
-                                    ${address.display()}
-                                </div>
-                                <div class="form-row">
-                                    <ul class="manage-table-actions">
-                                       <li>
-                                            %if not address.deleted:
-                                                <a class="action-button"  href="${h.url_for( controller='user', action='edit_address', address_id=address.id, 
-                                                                                             short_desc=address.desc,
-                                                                                             name=address.name, institution=address.institution, 
-                                                                                             address1=address.address, city=address.city, 
-                                                                                             state=address.state, postal_code=address.postal_code, 
-                                                                                             country=address.country, phone=address.phone)}">
-                                                                                             <span>Edit</span></a>
-                                                <a class="action-button"  href="${h.url_for( controller='user', action='delete_address', address_id=address.id)}">
-                                                <span>Delete address</span></a>
-                                            %else:
-                                                <a class="action-button"  href="${h.url_for( controller='user', action='undelete_address', address_id=address.id)}">
-                                                <span>Undelete address</span></a>
-                                            %endif
-                                            
-                                      </li>
-                                    </ul>
-                                </div>
-                            </td>
-                         </tr>             
-                    %endfor
-                </tbody>
-            </table>
-        %endif
+%if not addresses:
+    <label>There are no addresses</label>
+%else:
+    <div class="toolForm">
+        <div class="toolFormBody">
+            <% trans.user.refresh() %>
+                <table class="grid">
+                    <tbody>
+                        %for index, address in enumerate(addresses):    
+                            <tr class="libraryRow libraryOrFolderRow" id="libraryRow">
+                                <td>
+                                    <div class="form-row">   
+                                        <label>${address.desc}</label>
+                                        ${address.display()}
+                                    </div>
+                                    <div class="form-row">
+                                        <ul class="manage-table-actions">
+                                           <li>
+                                                %if not address.deleted:
+                                                    <a class="action-button"  href="${h.url_for( controller='user', action='edit_address', address_id=address.id, 
+                                                                                                 short_desc=address.desc,
+                                                                                                 name=address.name, institution=address.institution, 
+                                                                                                 address1=address.address, city=address.city, 
+                                                                                                 state=address.state, postal_code=address.postal_code, 
+                                                                                                 country=address.country, phone=address.phone)}">
+                                                                                                 <span>Edit</span></a>
+                                                    <a class="action-button"  href="${h.url_for( controller='user', action='delete_address', address_id=address.id)}">
+                                                    <span>Delete</span></a>
+                                                %else:
+                                                    <a class="action-button"  href="${h.url_for( controller='user', action='undelete_address', address_id=address.id)}">
+                                                    <span>Undelete</span></a>
+                                                %endif
+                                                
+                                          </li>
+                                        </ul>
+                                    </div>
+                                </td>
+                             </tr>             
+                        %endfor
+                    </tbody>
+                </table>
+            %endif
+        </div>
     </div>
-</div>
 %endif
\ No newline at end of file
diff -r fbad627b45ac -r e6dda627e6b0 test/base/twilltestcase.py
--- a/test/base/twilltestcase.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/test/base/twilltestcase.py	Sat Aug 22 23:20:09 2009 -0400
@@ -972,7 +972,7 @@
         self.home()
# Form stuff
-    def create_form( self, name='Form One', description='This is Form One', num_fields=1 ):
+    def create_form( self, name='Form One', desc='This is Form One', num_fields=1 ):
         """
         Create a new form definition.  Testing framework is still limited to only testing
         one instance for each repeat. This has to do with the 'flat' nature of defining
@@ -988,7 +988,7 @@
         self.visit_url( "%s/forms/new" % self.url )
         self.check_page_for_string( 'Create a new form definition' )
         tc.fv( "1", "name", name ) # form field 1 is the field named name...
-        tc.fv( "1", "description", description ) # form field 1 is the field named name...
+        tc.fv( "1", "description", desc ) # form field 1 is the field named name...
         tc.submit( "create_form_button" )
         for index in range( num_fields ):
             field_name = 'field_name_%i' % index
@@ -1001,7 +1001,140 @@
             check_str = "The form '%s' has been updated with the changes." % name
         self.check_page_for_string( check_str )
         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)"):
+        """
+        Edit form details; name & description
+        """
+        self.home()
+        self.visit_url( "%s/forms/edit?form_id=%i&show_form=True" % (self.url, form_id) )
+        self.check_page_for_string( 'Edit form definition "%s"' % form_name )
+        tc.fv( "1", "name", new_form_name ) 
+        tc.fv( "1", "description", new_form_desc ) 
+        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):
+        """
+        Add a new fields to the form definition
+        """
+        self.home()
+        self.visit_url( "%s/forms/edit?form_id=%i&show_form=True" % (self.url, form_id) )
+        self.check_page_for_string( 'Edit form definition "%s"' % form_name)
+        for i, field in enumerate(fields):
+            index = i+field_index
+            tc.submit( "add_field_button" )
+            tc.fv( "1", "field_name_%i" % index, field['name'] )
+            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 )
+        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 )
+        self.home()
+    def form_remove_field( self, form_id, form_name, field_name):
+        """
+        Remove a field from the form definition
+        """
+        self.home()
+        self.visit_url( "%s/forms/edit?form_id=%i&show_form=True" % (self.url, form_id) )
+        self.check_page_for_string( 'Edit form definition "%s"' % form_name)
+        tc.submit( "remove_button" )
+        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 )
+        self.home()
+    # Requests stuff
+    def create_request_type( self, name, desc, request_form_id, sample_form_id, states ):
+        self.home()
+        self.visit_url( "%s/admin/request_type?create=True" % self.url )
+        self.check_page_for_string( 'Create a new request type' )
+        tc.fv( "1", "name", name )
+        tc.fv( "1", "description", desc )
+        tc.fv( "1", "request_form_id", request_form_id )
+        tc.fv( "1", "sample_form_id", sample_form_id )
+        tc.fv( "1", "num_states", str( len( states ) ) )
+        tc.submit( "define_states_button" )
+        self.check_page_for_string( "Create %i states for the '%s' request type" % ( len(states), name ))
+        for index, state in enumerate(states):
+            tc.fv("1", "state_name_%i" % index, state[0])
+            tc.fv("1", "state_desc_%i" % index, state[1])
+        tc.submit( "save_request_type" )
+        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, fields ):
+        self.home()
+        self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % (self.url, request_type_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) )
+        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.check_page_for_string( 'Add a new request' )
+        tc.fv( "1", "select_user", str(user_id) )
+        tc.fv( "1", "name", name )
+        tc.fv( "1", "desc", desc )
+        tc.fv( "1", "library_id", str(library_id) )
+        for index, field_value in enumerate(fields):
+            tc.fv( "1", "field_%i" % index, field_value )
+        tc.submit( "create_request_button" )
+    def edit_request( self, request_id, name, new_name, new_desc, new_library_id, new_fields):
+        self.home()
+        self.visit_url( "%s/requests/edit?request_id=%i&show=True" % (self.url, request_id) )
+        self.check_page_for_string( 'Edit request "%s"' % name )
+        tc.fv( "1", "name", new_name )
+        tc.fv( "1", "desc", new_desc )
+        tc.fv( "1", "library_id", str(new_library_id) )
+        for index, field_value in enumerate(new_fields):
+            tc.fv( "1", "field_%i" % index, field_value )
+        tc.submit( "save_changes_request_button" )
+    def add_samples( self, request_id, request_name, samples ):
+        self.home()
+        self.visit_url( "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) ))
+        self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
+        for sample_index, sample in enumerate(samples):
+            tc.submit( "add_sample_button" )
+            sample_name, fields = sample
+            tc.fv( "1", "sample_%i_name" % sample_index, sample_name )
+            for field_index, field_value in enumerate(fields):
+                tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value )
+        tc.submit( "save_samples_button" )
+    def submit_request( self, request_id, request_name ):
+        self.home()
+        self.visit_url( "%s/requests/submit_request?id=%i" % ( self.url, request_id ))
+        self.check_page_for_string( 'The request <b>%s</b> has been submitted.' % request_name )
+    def add_bar_codes( self, request_id, request_name, bar_codes ):
+        self.home()
+        self.visit_url( "%s/requests_admin/bar_codes?request_id=%i" % (self.url, request_id) )
+        self.check_page_for_string( 'Bar codes for Samples of Request "%s"' % request_name )
+        for index, bar_code in enumerate(bar_codes):
+            tc.fv( "1", "sample_%i_bar_code" % index, bar_code )
+        tc.submit( "save_bar_codes" )
+    def change_sample_state( self, sample_name, sample_id, new_state_id, comment='' ):
+        self.home()
+        self.visit_url( "%s/requests_admin/show_events?sample_id=%i" % (self.url, sample_id) )
+        self.check_page_for_string( 'Events for Sample "%s"' % sample_name )
+        tc.fv( "1", "select_state", str(new_state_id) )
+        tc.fv( "1", "comment", comment )
+        tc.submit( "add_event_button" )
+    # Address stuff
+    def create_address( self, address ):
+        self.home()
+        self.visit_url( "%s/user/new_address" % self.url )
+        self.check_page_for_string( 'New address' )
+        for name, value in address.iteritems():
+            tc.fv( "1", name, value )
+        tc.submit( "Save_button" )
     # Library stuff
     def create_library( self, name='Library One', description='This is Library One' ):
         """Create a new library"""
diff -r fbad627b45ac -r e6dda627e6b0 test/functional/test_forms_and_requests.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/functional/test_forms_and_requests.py	Sat Aug 22 23:20:09 2009 -0400
@@ -0,0 +1,274 @@
+import galaxy.model
+from galaxy.model.orm import *
+from base.twilltestcase import *
+
+not_logged_in_as_admin_security_msg = 'You must be logged in as an administrator to access this feature.'
+logged_in_as_admin_security_msg = 'You must be an administrator to access this feature.'
+not_logged_in_security_msg = 'You must be logged in to create/submit sequencing requests'
+form_one_name = "Request Form"
+form_two_name = "Sample Form"
+request_type_name = 'Test Requestype'
+sample_states = [  ( 'New', 'Sample entered into the system' ), 
+                   ( 'Received', 'Sample tube received' ), 
+                   ( 'Done', 'Sequence run complete' ) ]
+address1 = dict(  short_desc="Office",
+                  name="James Bond",
+                  institution="MI6" ,
+                  address1="MI6 Headquaters",
+                  address2="",
+                  city="London",
+                  state="London",
+                  postal_code="007",
+                  country="United Kingdom",
+                  phone="007-007-0007" )
+
+
+def get_latest_form(form_name):
+    fdc_list = galaxy.model.FormDefinitionCurrent.filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False )\
+                                        .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() )
+    for fdc in fdc_list:
+        if form_name == fdc.latest_form.name:
+            return fdc.latest_form
+    return None
+
+
+class TestFormsAndRequests( TwillTestCase ):
+    def test_000_create_form( self ):
+        """Testing creating a new form and editing it"""
+        self.logout()
+        self.login( email='test@bx.psu.edu' )
+        # create a form
+        global form_one_name
+        name = form_one_name
+        desc = "This is Form One's description"
+        self.create_form( name=name, desc=desc )
+        self.home()
+        self.visit_page( 'forms/manage' )
+        self.check_page_for_string( name )
+        self.check_page_for_string( desc )
+        # 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 ) ).all()[-1]
+        assert form_one is not None, 'Problem retrieving form named "%s" from the database' % name
+        # edit form & add few more fields
+        new_name = "Request Form (Renamed)"
+        new_desc = "This is Form One's Re-described"
+        self.edit_form( form_one.id, form_one.name, new_form_name=new_name, new_form_desc=new_desc )
+        self.home()
+        self.visit_page( 'forms/manage' )
+        self.check_page_for_string( new_name )
+        self.check_page_for_string( new_desc )
+        form_one_name = new_name
+    def test_005_add_form_fields( self ):
+        """Testing adding fields to a form definition"""
+        fields = [dict(name='Test field name one',
+                       desc='Test field description one',
+                       type='TextField',
+                       required='required'),
+                  dict(name='Test field name two',
+                       desc='Test field description two',
+                       type='AddressField',
+                       required='optional')]
+        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)
+        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
+        name = form_two_name
+        desc = "This is Form One's description"
+        self.create_form( name=name, desc=desc )
+        self.home()
+        self.visit_page( 'forms/manage' )
+        self.check_page_for_string( name )
+        self.check_page_for_string( desc )
+    def test_020_create_request_type( self ):
+        """Testing creating a new requestype"""
+        request_form = get_latest_form(form_one_name)
+        sample_form = get_latest_form(form_two_name)
+        self.create_request_type(request_type_name, "test request type", 
+                                 str(request_form.id), str(sample_form.id), sample_states )
+        global request_type
+        request_type = galaxy.model.RequestType.filter( and_( galaxy.model.RequestType.table.c.name==request_type_name ) ).all()[-1]
+        assert request_type is not None, 'Problem retrieving request type named "%s" from the database' % request_type_name
+    def test_025_create_address_and_library( self ):
+        """Testing address & library creation"""
+        # first create a regular user
+        self.logout()
+        self.login( email='test1@bx.psu.edu' )
+        self.logout()
+        self.login( email='test@bx.psu.edu' )
+        # first create a library for the request so that it can be submitted later
+        lib_name = 'TestLib001'
+        self.create_library( lib_name, '' )
+        self.visit_page( 'admin/browse_libraries' )
+        self.check_page_for_string( lib_name )
+        # Get the library object for later tests
+        global library_one
+        library_one = galaxy.model.Library.filter( and_( galaxy.model.Library.table.c.name==lib_name,
+                                                         galaxy.model.Library.table.c.deleted==False ) ).first()
+        assert library_one is not None, 'Problem retrieving library named "%s" from the database' % lib_name
+        global admin_user
+        admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test@bx.psu.edu' ).first()
+        assert admin_user is not None, 'Problem retrieving user with email "test@bx.psu.edu" from the database'
+        # Get the admin user's private role for later use
+        global admin_user_private_role
+        admin_user_private_role = None
+        for role in admin_user.all_roles():
+            if role.name == admin_user.email and role.description == 'Private Role for %s' % admin_user.email:
+                admin_user_private_role = role
+                break
+        if not admin_user_private_role:
+            raise AssertionError( "Private role not found for user '%s'" % admin_user.email )
+        global regular_user1
+        regular_user1 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1@bx.psu.edu' ).first()
+        assert regular_user1 is not None, 'Problem retrieving user with email "test1@bx.psu.edu" from the database'
+        # Get the regular user's private role for later use
+        global regular_user1_private_role
+        regular_user1_private_role = None
+        for role in regular_user1.all_roles():
+            if role.name == regular_user1.email and role.description == 'Private Role for %s' % regular_user1.email:
+                regular_user1_private_role = role
+                break
+        if not regular_user1_private_role:
+            raise AssertionError( "Private role not found for user '%s'" % regular_user1.email )
+        # Set permissions on the library, sort for later testing
+        permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ]
+        permissions_out = []
+        # Role one members are: admin_user, regular_user1.  Each of these users will be permitted to
+        # LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE for library items.
+        self.set_library_permissions( str( library_one.id ), library_one.name, str( regular_user1_private_role.id ), permissions_in, permissions_out )
+        # create address
+        #self.create_address( user_address1 )
+        #self.check_page_for_string( 'Address <b>%s</b> has been added' % user_address1[ 'short_desc' ] )
+        ## TODO: FIX HACK
+        ## the user address creation should be done as a test. 
+        global user_address
+        user_address = galaxy.model.UserAddress()
+        user_address.user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1@bx.psu.edu' ).first()
+        user_address.desc = address1[ 'short_desc' ]
+        user_address.name = address1[ 'name' ]
+        user_address.institution = address1[ 'institution' ]
+        user_address.address = address1[ 'address1' ]+' '+address1[ 'address2' ]
+        user_address.city = address1[ 'city' ]
+        user_address.state = address1[ 'state' ]
+        user_address.postal_code = address1[ 'postal_code' ]
+        user_address.country = address1[ 'country' ]
+        user_address.phone = address1[ 'phone' ]
+        user_address.flush()
+        user_address.user.refresh()
+    def test_030_create_request( self ):
+        """Testing creating, editing and submitting a request as a regular user"""
+        # login as a regular user
+        self.logout()
+        self.login( email='test1@bx.psu.edu' )
+        # set field values
+        fields = ['field one value', 'field two value', str(user_address.id)] 
+        # 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, fields)
+        self.check_page_for_string( request_name )
+        self.check_page_for_string( request_desc )
+        global request_one
+        request_one = galaxy.model.Request.filter( and_( galaxy.model.Request.table.c.name==request_name,
+                                                         galaxy.model.Request.table.c.deleted==False ) ).first()        
+        # check if the request's state is now set to 'unsubmitted'
+        assert request_one.state is not request_one.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.UNSUBMITTED )
+        # sample fields
+        samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ),
+                    ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ]
+        # add samples to this request
+        self.add_samples( request_one.id, request_one.name, samples )
+        for sample_name, fields in samples:
+            self.check_page_for_string( sample_name )
+            self.check_page_for_string( 'Unsubmitted' )
+            for field_value in fields:
+                self.check_page_for_string( field_value )
+        # edit this request
+        fields = ['field one value (editted)', 'field two value (editted)', 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, fields)
+        request_one.refresh()
+        self.check_page_for_string( request_name+' (Renamed)' )
+        self.check_page_for_string( request_desc+' (Re-described)' )
+        # submit the request
+        self.submit_request( request_one.id, request_one.name )
+        request_one.refresh()
+        # check if the request's state is now set to 'submitted'
+        assert request_one.state is not request_one.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.SUBMITTED )
+    def test_035_request_lifecycle( self ):
+        """Testing request lifecycle as it goes through all the states"""
+        # goto admin manage requests page
+        self.logout()
+        self.login( email='test@bx.psu.edu' )
+        self.home()
+        self.visit_page( 'requests_admin/list' )
+        self.check_page_for_string( request_one.name )
+        self.visit_url( "%s/requests_admin/list?sort=-create_time&operation=show_request&id=%s" \
+                        % ( self.url, self.security.encode_id( request_one.id ) ))
+        self.check_page_for_string( 'Sequencing Request "%s"' % request_one.name )
+        # set bar codes for the samples
+        bar_codes = [ '1234567890', '0987654321' ]
+        self.add_bar_codes( request_one.id, request_one.name, bar_codes )
+        self.check_page_for_string( 'Bar codes has been saved for this request' )
+        # change the states of all the samples of this request
+        for sample in request_one.samples:
+            self.change_sample_state( sample.name, sample.id, request_type.states[1].id )
+            self.check_page_for_string( request_type.states[1].name )
+            self.check_page_for_string( request_type.states[1].desc )
+            self.change_sample_state( sample.name, sample.id, request_type.states[2].id )
+            self.check_page_for_string( request_type.states[2].name )
+            self.check_page_for_string( request_type.states[2].desc )
+        self.home()
+        request_one.refresh()
+        # check if the request's state is now set to 'complete'
+        assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.COMPLETE )
+#    def test_40_admin_create_request_on_behalf_of_regular_user( self ):
+#        """Testing creating and submitting a request as an admin on behalf of a regular user"""
+#        self.logout()
+#        self.login( email='test@bx.psu.edu' )
+##        permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ]
+##        permissions_out = []
+##        self.set_library_permissions( str( library_one.id ), library_one.name, str( admin_user_private_role.id ), permissions_in, permissions_out )
+#        # set field values
+#        fields = ['field one value', 'field two value', str(user_address.id)] 
+#        # create the request
+#        request_name, request_desc = 'Request Two', 'Request Two Description'
+#        self.create_request_admin(request_type.id, regular_user1.id, request_name, request_desc, library_one.id, fields)
+#        self.check_page_for_string( request_name )
+#        self.check_page_for_string( request_desc )
+#        global request_two
+#        request_one = galaxy.model.Request.filter( and_( galaxy.model.Request.table.c.name==request_name,
+#                                                         galaxy.model.Request.table.c.deleted==False ) ).first()        
+#        # check if the request's state is now set to 'unsubmitted'
+#        assert request_two.state is not request_two.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.UNSUBMITTED )
+#        # sample fields
+#        samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ),
+#                    ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ]
+#        # add samples to this request
+#        self.add_samples( request_two.id, request_two.name, samples )
+#        for sample_name, fields in samples:
+#            self.check_page_for_string( sample_name )
+#            self.check_page_for_string( 'Unsubmitted' )
+#            for field_value in fields:
+#                self.check_page_for_string( field_value )
+#        # submit the request
+#        self.submit_request( request_two.id, request_two.name )
+#        request_two.refresh()
+#        # check if the request's state is now set to 'submitted'
+#        assert request_two.state is not request_two.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" % ( request_two.name, request_two.states.SUBMITTED )
+
+        
+        
+        
+        
+        
+        
\ No newline at end of file
diff -r fbad627b45ac -r e6dda627e6b0 test/functional/test_security_and_libraries.py
--- a/test/functional/test_security_and_libraries.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/test/functional/test_security_and_libraries.py	Sat Aug 22 23:20:09 2009 -0400
@@ -196,7 +196,7 @@
         dhps.sort()
         # Compare DefaultHistoryPermissions and actions_in - should be the same
         if dhps != actions_in:
-                raise AssertionError( 'DefaultHistoryPermissions "%s" for history id %d differ from actions "%s" passed for changing' \
+            raise AssertionError( 'DefaultHistoryPermissions "%s" for history id %d differ from actions "%s" passed for changing' \
                                       % ( str( dhps ), latest_history.id, str( actions_in ) ) )
         # Make sure DatasetPermissionss are correct
         if len( latest_dataset.actions ) != len( latest_history.default_permissions ):
@@ -209,7 +209,7 @@
         dps.sort()
         # Compare DatasetPermissionss and DefaultHistoryPermissions - should be the same
         if dps != dhps:
-                raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from DefaultHistoryPermissions "%s"' \
+            raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from DefaultHistoryPermissions "%s"' \
                                       % ( str( dps ), latest_dataset.id, str( dhps ) ) )
         self.logout()
     def test_020_create_new_user_account_as_admin( self ):
diff -r fbad627b45ac -r e6dda627e6b0 tools/extract/liftOver_wrapper_code.py
--- a/tools/extract/liftOver_wrapper_code.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/tools/extract/liftOver_wrapper_code.py	Sat Aug 22 23:20:09 2009 -0400
@@ -3,7 +3,6 @@
     to_dbkey = param_dict['to_dbkey'].split('.')[0].split('To')[1]
     to_dbkey = to_dbkey[0].lower()+to_dbkey[1:]
     out_data['out_file1'].set_dbkey(to_dbkey)
-    out_data['out_file2'].set_dbkey(to_dbkey)
     out_data['out_file1'].name = out_data['out_file1'].name + " [ MAPPED COORDINATES ]"
     out_data['out_file2'].name = out_data['out_file2'].name + " [ UNMAPPED COORDINATES ]"
diff -r fbad627b45ac -r e6dda627e6b0 tools/metag_tools/split_paired_reads.py
--- a/tools/metag_tools/split_paired_reads.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/tools/metag_tools/split_paired_reads.py	Sat Aug 22 23:20:09 2009 -0400
@@ -1,7 +1,7 @@
 #! /usr/bin/python
"""
-Split Solexa paired end reads
+Split fixed length paired end reads
 """
import os, sys
@@ -12,9 +12,13 @@
     outfile_end1 = open(sys.argv[2], 'w')
     outfile_end2 = open(sys.argv[3], 'w')
-    for i, line in enumerate(file(infile)):
+    i = 0
+    
+    for line in file( infile ):
         line = line.rstrip()
-        if not line or line.startswith('#'): continue
+        
+        if not line:
+            continue
end1 = ''
         end2 = ''
@@ -42,5 +46,9 @@
         outfile_end1.write('%s\n' %(end1))
         outfile_end2.write('%s\n' %(end2))
+        i += 1
+        
+    if  i % 4 != 0  :
+        sys.stderr.write("WARNING: Number of lines in the input file was not divisible by 4.\nCheck consistency of the input fastq file.\n")
     outfile_end1.close()
     outfile_end2.close()    
\ No newline at end of file
diff -r fbad627b45ac -r e6dda627e6b0 tools/solid_tools/maq_cs_wrapper.py
--- a/tools/solid_tools/maq_cs_wrapper.py	Sat Aug 22 23:18:47 2009 -0400
+++ b/tools/solid_tools/maq_cs_wrapper.py	Sat Aug 22 23:20:09 2009 -0400
@@ -48,9 +48,9 @@
         cmd1 = "solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,tmps.name,f3_read_fname,f3_qual_fname,r3_read_fname,r3_qual_fname)
         try:
             os.system(cmd1)
-            os.system('zcat -f %s >> %s' %(tmpf.name,tmpffastq.name))
-            os.system('zcat -f %s >> %s' %(tmpr.name,tmprfastq.name))
-            os.system('zcat -f %s >> %s' %(tmps.name,tmpsfastq.name))
+            os.system('gunzip -c %s >> %s' %(tmpf.name,tmpffastq.name))
+            os.system('gunzip -c %s >> %s' %(tmpr.name,tmprfastq.name))
+            os.system('gunzip -c %s >> %s' %(tmps.name,tmpsfastq.name))
except Exception, eq:
             stop_err("Error converting data to fastq format." + str(eq))
@@ -135,7 +135,7 @@
         cmd1 = "solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,None,None,f3_read_fname,f3_qual_fname,None,None)
         try:
             os.system(cmd1)
-            os.system('zcat -f %s >> %s' %(tmpf.name,tmpfastq.name))
+            os.system('gunzip -c %s >> %s' %(tmpf.name,tmpfastq.name))
             tmpf.close()
         except:
             stop_err("Error converting data to fastq format.")

    

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[galaxy-dev] [hg] galaxy 2606: Merge