mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Forms & request controllers
- refactored to work on main - cleanup Added more functional tests
This commit is contained in:
Ramkrishna Chakrabarty
@@ -1090,11 +1090,12 @@ class FormDefinition( object ):
|
||||
types = Bunch( REQUEST = 'Sequencing Request Form',
|
||||
SAMPLE = 'Sequencing Sample Form',
|
||||
LIBRARY_INFO_TEMPLATE = 'Library information template' )
|
||||
def __init__(self, name=None, desc=None, fields=[], current_form=None, form_type=None, layout=None):
|
||||
def __init__(self, name=None, desc=None, fields=[],
|
||||
form_definition_current=None, form_type=None, layout=None):
|
||||
self.name = name
|
||||
self.desc = desc
|
||||
self.fields = fields
|
||||
self.form_definition_current = current_form
|
||||
self.form_definition_current = form_definition_current
|
||||
self.type = form_type
|
||||
self.layout = layout
|
||||
def fields_of_grid(self, layout_grid_name):
|
||||
@@ -1263,20 +1264,26 @@ class UserAddress( object ):
|
||||
self.postal_code = postal_code
|
||||
self.country = country
|
||||
self.phone = phone
|
||||
def display(self):
|
||||
return self.name+'<br/>'+ \
|
||||
self.institution+'<br/>'+ \
|
||||
self.address+'<br/>'+ \
|
||||
self.city+' '+self.state+' '+self.postal_code+'<br/>'+ \
|
||||
self.country+'<br/>'+ \
|
||||
'Phone: '+self.phone
|
||||
def get_html(self):
|
||||
return self.name+'<br/>'+ \
|
||||
self.institution+'<br/>'+ \
|
||||
self.address+'<br/>'+ \
|
||||
self.city+' '+self.state+' '+self.postal_code+'<br/>'+ \
|
||||
self.country+'<br/>'+ \
|
||||
'Phone: '+self.phone
|
||||
html = ''
|
||||
if self.name:
|
||||
html = html + self.name
|
||||
if self.institution:
|
||||
html = html + '<br/>' + self.institution
|
||||
if self.address:
|
||||
html = html + '<br/>' + self.address
|
||||
if self.city:
|
||||
html = html + '<br/>' + self.city
|
||||
if self.state:
|
||||
html = html + ' ' + self.state
|
||||
if self.postal_code:
|
||||
html = html + ' ' + self.postal_code
|
||||
if self.country:
|
||||
html = html + '<br/>' + self.country
|
||||
if self.phone:
|
||||
html = html + '<br/>' + 'Phone: ' + self.phone
|
||||
return html
|
||||
|
||||
|
||||
class Page( object ):
|
||||
def __init__( self ):
|
||||
|
||||
+207
-137
@@ -12,6 +12,14 @@ import copy
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
class Forms( BaseController ):
|
||||
# Empty form field
|
||||
empty_field = { 'label': '',
|
||||
'helptext': '',
|
||||
'visible': True,
|
||||
'required': False,
|
||||
'type': BaseField.form_field_types()[0],
|
||||
'selectlist': [],
|
||||
'layout': 'none' }
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def index( self, trans, **kwd ):
|
||||
@@ -84,19 +92,12 @@ class Forms( BaseController ):
|
||||
action='edit',
|
||||
form_id=fd.id,
|
||||
add_field_button='Add field',
|
||||
num_fields=0,
|
||||
name=fd.name,
|
||||
description=fd.desc,
|
||||
form_type_selectbox=fd.type ) )
|
||||
self.current_form = {}
|
||||
self.current_form[ 'name' ] = 'New Form'
|
||||
self.current_form[ 'desc' ] = ''
|
||||
self.current_form[ 'type' ] = params.get( 'form_type', 'none' )
|
||||
self.current_form[ 'layout' ] = [ 'Main' ]
|
||||
self.current_form[ 'fields' ] = []
|
||||
inputs = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ),
|
||||
( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ),
|
||||
( 'Type', self.__form_types_widget(trans, selected=self.current_form['type']) ),
|
||||
inputs = [ ( 'Name', TextField( 'name', 40, 'New Form' ) ),
|
||||
( 'Description', TextField( 'description', 40, '' ) ),
|
||||
( 'Type', self.__form_types_widget(trans, selected=params.get( 'form_type', 'none' )) ),
|
||||
( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ]
|
||||
return trans.fill_template( '/admin/forms/create_form.mako',
|
||||
inputs=inputs,
|
||||
@@ -134,102 +135,156 @@ class Forms( BaseController ):
|
||||
renaming fields, adding/deleting fields, changing fields attributes.
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
log.debug( kwd )
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
form_id = params.get( 'form_id', None )
|
||||
if not form_id:
|
||||
msg = 'Invalid form id %s' % str( form_id )
|
||||
trans.response.send_redirect( web.url_for( controller='forms',
|
||||
action='manage',
|
||||
msg=msg,
|
||||
messagetype='error' ) )
|
||||
fd = trans.app.model.FormDefinition.get( int( params.form_id ) )
|
||||
try:
|
||||
fd = trans.app.model.FormDefinition.get( int( params.get( 'form_id', None ) ) )
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='forms',
|
||||
action='manage',
|
||||
msg='Invalid form',
|
||||
messagetype='error' ) )
|
||||
#
|
||||
# Show the form for editing
|
||||
#
|
||||
if params.get( 'show_form', False ):
|
||||
self.__get_saved_form( fd )
|
||||
# The following two dicts store the unsaved select box options
|
||||
self.del_options = {}
|
||||
self.add_options = {}
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
|
||||
#Add a layout grid
|
||||
current_form = self.__get_saved_form( fd )
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype=messagetype, **kwd )
|
||||
#
|
||||
# Add a layout grid
|
||||
#
|
||||
elif params.get( 'add_layout_grid', False ):
|
||||
self.__update_current_form( trans, **kwd )
|
||||
self.__add_layout_grid()
|
||||
current_form = self.__get_form( trans, **kwd )
|
||||
current_form['layout'].append('')
|
||||
# show the form again
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype=messagetype, **kwd )
|
||||
#
|
||||
# Delete a layout grid
|
||||
#
|
||||
elif params.get( 'remove_layout_grid_button', False ):
|
||||
self.__update_current_form( trans, **kwd )
|
||||
current_form = self.__get_form( trans, **kwd )
|
||||
index = int( kwd[ 'remove_layout_grid_button' ].split( ' ' )[2] ) - 1
|
||||
self.__remove_layout_grid( index )
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
|
||||
# Delete a field
|
||||
elif params.get( 'remove_button', False ):
|
||||
self.__update_current_form( trans, **kwd )
|
||||
index = int( kwd[ 'remove_button' ].split( ' ' )[2] ) - 1
|
||||
self.__remove_field( index )
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
|
||||
# Save changes
|
||||
elif params.get( 'save_changes_button', False ):
|
||||
self.__update_current_form( trans, **kwd )
|
||||
fd_new, msg = self.__save_form( trans, fd.form_definition_current.id, **kwd )
|
||||
if not fd_new:
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype='error', **kwd )
|
||||
else:
|
||||
fd = fd_new
|
||||
msg = "The form '%s' has been updated with the changes." % fd.name
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
|
||||
#Add a field
|
||||
del current_form['layout'][index]
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype=messagetype, **kwd )
|
||||
#
|
||||
# Add a field
|
||||
#
|
||||
elif params.get( 'add_field_button', False ):
|
||||
self.__update_current_form( trans, **kwd )
|
||||
self.__add_field()
|
||||
current_form = self.__get_form( trans, **kwd )
|
||||
current_form['fields'].append( self.empty_field )
|
||||
# show the form again with one empty field
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype=messagetype, **kwd )
|
||||
#
|
||||
# Delete a field
|
||||
#
|
||||
elif params.get( 'remove_button', False ):
|
||||
current_form = self.__get_form( trans, **kwd )
|
||||
# find the index of the field to be removed from the remove button label
|
||||
index = int( kwd[ 'remove_button' ].split( ' ' )[2] ) - 1
|
||||
del current_form['fields'][index]
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype=messagetype, **kwd )
|
||||
#
|
||||
# Save changes
|
||||
#
|
||||
elif params.get( 'save_changes_button', False ):
|
||||
fd_new, msg = self.__save_form( trans, fdc_id=fd.form_definition_current.id, **kwd )
|
||||
# if validation error encountered while saving the form, show the
|
||||
# unsaved form, with the error message
|
||||
if not fd_new:
|
||||
current_form = self.__get_form( trans, **kwd )
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype='error', **kwd )
|
||||
# everything went fine. form saved successfully. Show the saved form
|
||||
fd = fd_new
|
||||
current_form = self.__get_saved_form( fd )
|
||||
msg = "The form '%s' has been updated with the changes." % fd.name
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype=messagetype, **kwd )
|
||||
#
|
||||
# Show form read-only
|
||||
#
|
||||
elif params.get( 'read_only', False ):
|
||||
return trans.fill_template( '/admin/forms/show_form_read_only.mako',
|
||||
form=fd,
|
||||
msg=msg,
|
||||
messagetype=messagetype )
|
||||
# Refresh page, SelectField is selected/deselected as the type of a field
|
||||
elif params.get( 'refresh', False ):
|
||||
self.__update_current_form( trans, **kwd )
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
|
||||
# Remove SelectField option
|
||||
elif params.get( 'select_box_options', False ) == 'remove':
|
||||
index = int( kwd[ 'field_index' ] )
|
||||
option = int( kwd[ 'option_index' ] )
|
||||
del self.current_form[ 'fields' ][ index ][ 'selectlist' ][ option ]
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
|
||||
#
|
||||
# Add SelectField option
|
||||
elif params.get( 'select_box_options', False ) == 'add':
|
||||
index = int( kwd[ 'field_index' ] )
|
||||
self.current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' )
|
||||
return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd )
|
||||
def __add_layout_grid(self):
|
||||
self.current_form['layout'].append('')
|
||||
def __remove_layout_grid(self, index):
|
||||
del self.current_form['layout'][index]
|
||||
def __remove_field(self, index):
|
||||
del self.current_form['fields'][index]
|
||||
def __add_field(self):
|
||||
#
|
||||
elif 'Add' in kwd.values():
|
||||
return self.__add_selectbox_option(trans, fd, msg, messagetype, **kwd)
|
||||
#
|
||||
# Remove SelectField option
|
||||
#
|
||||
elif 'Remove' in kwd.values():
|
||||
return self.__remove_selectbox_option(trans, fd, msg, messagetype, **kwd)
|
||||
#
|
||||
# Refresh page
|
||||
#
|
||||
elif params.get( 'refresh', False ):
|
||||
current_form = self.__get_form( trans, **kwd )
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype=messagetype, **kwd )
|
||||
|
||||
def __add_selectbox_option( self, trans, fd, msg, messagetype, **kwd ):
|
||||
'''
|
||||
add an empty field to the fields list
|
||||
This method adds a selectbox option. The kwd dict searched for
|
||||
the field index which needs to be removed
|
||||
'''
|
||||
empty_field = { 'label': '',
|
||||
'helptext': '',
|
||||
'visible': True,
|
||||
'required': False,
|
||||
'type': BaseField.form_field_types()[0],
|
||||
'selectlist': [],
|
||||
'layout': 'none' }
|
||||
self.current_form['fields'].append(empty_field)
|
||||
current_form = self.__get_form( trans, **kwd )
|
||||
index = -1
|
||||
for k, v in kwd.items():
|
||||
if v == 'Add':
|
||||
# extract the field index from the
|
||||
# button name of format: 'addoption_<field>'
|
||||
index = int(k.split('_')[1])
|
||||
break
|
||||
if index == -1:
|
||||
# something wrong happened
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg='Error in adding selectfield option',
|
||||
messagetype='error', **kwd )
|
||||
# add an empty option
|
||||
current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' )
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype=messagetype, **kwd )
|
||||
def __remove_selectbox_option( self, trans, fd, msg, messagetype, **kwd ):
|
||||
'''
|
||||
This method removes a selectbox option. The kwd dict searched for
|
||||
the field index and option index which needs to be removed
|
||||
'''
|
||||
current_form = self.__get_form( trans, **kwd )
|
||||
option = -1
|
||||
for k, v in kwd.items():
|
||||
if v == 'Remove':
|
||||
# extract the field & option indices from the
|
||||
# button name of format: 'removeoption_<field>_<option>'
|
||||
index = int(k.split('_')[1])
|
||||
option = int(k.split('_')[2])
|
||||
break
|
||||
if option == -1:
|
||||
# something wrong happened
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg='Error in removing selectfield option',
|
||||
messagetype='error', **kwd )
|
||||
# remove the option
|
||||
del current_form[ 'fields' ][ index ][ 'selectlist' ][ option ]
|
||||
return self.__show( trans=trans, form=fd, current_form=current_form,
|
||||
msg=msg, messagetype=messagetype, **kwd )
|
||||
|
||||
|
||||
def __get_field(self, index, **kwd):
|
||||
'''
|
||||
This method retrieves all the user-entered details of a field and
|
||||
returns a dict.
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
#TODO: RC this needs to be handled so that it does not throw an exception.
|
||||
# To reproduce, create a new form, click the "add field" button, click the
|
||||
# browser back arrow, then click the "add field" button again.
|
||||
# You should never attempt to "restore_text()" on a None object...
|
||||
name = util.restore_text( params.get( 'field_name_%i' % index, '' ) )
|
||||
helptext = util.restore_text( params.get( 'field_helptext_%i' % index, '' ) )
|
||||
required = params.get( 'field_required_%i' % index, False )
|
||||
@@ -266,57 +321,54 @@ class Forms( BaseController ):
|
||||
else:
|
||||
return sb_options
|
||||
def __get_saved_form(self, fd):
|
||||
self.current_form = {}
|
||||
self.current_form['name'] = fd.name
|
||||
self.current_form['desc'] = fd.desc
|
||||
self.current_form['type'] = fd.type
|
||||
self.current_form['layout'] = list(copy.deepcopy(fd.layout))
|
||||
self.current_form['fields'] = list(copy.deepcopy(fd.fields))
|
||||
def __validate_form(self, **kwd):
|
||||
'''
|
||||
This method checks the following text inputs are filled out by the user
|
||||
- the name of form
|
||||
- name of all the fields
|
||||
This retrieves the saved form and returns a dictionary containing the name,
|
||||
desc, type, layout & fields of the form
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
# form name
|
||||
if not util.restore_text( params.name ):
|
||||
return None, 'Form name must be filled.'
|
||||
# form type
|
||||
if util.restore_text( params.form_type_selectbox ) == 'none':
|
||||
return None, 'Form type must be selected.'
|
||||
# fields
|
||||
# for i in range( len(self.current_form['fields']) ):
|
||||
# if not util.restore_text(params.get( 'field_name_%i' % i, None )):
|
||||
# return None, "All the field label(s) must be completed."
|
||||
return True, ''
|
||||
return dict(name = fd.name,
|
||||
desc = fd.desc,
|
||||
type = fd.type,
|
||||
layout = list(copy.deepcopy(fd.layout)),
|
||||
fields = list(copy.deepcopy(fd.fields)))
|
||||
def __get_form(self, trans, **kwd):
|
||||
'''
|
||||
This method gets all the user-entered form details and returns a
|
||||
dictionary containing the name, desc, type, layout & fields of the form
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
name = util.restore_text( params.name )
|
||||
desc = util.restore_text( params.description ) or ""
|
||||
form_type = util.restore_text( params.form_type_selectbox )
|
||||
# get the user entered layout grids
|
||||
layout = []
|
||||
if form_type == trans.app.model.FormDefinition.types.SAMPLE:
|
||||
for index in range(len(self.current_form[ 'layout' ])):
|
||||
layout.append(params.get( 'grid_layout%i' % index, '' ))
|
||||
index = 0
|
||||
while True:
|
||||
grid_name = util.restore_text( params.get( 'grid_layout%i' % index, '' ) )
|
||||
if grid_name:
|
||||
layout.append( grid_name )
|
||||
index = index + 1
|
||||
else:
|
||||
break
|
||||
# for csv file import
|
||||
csv_file = params.get( 'file_data', '' )
|
||||
fields = []
|
||||
if csv_file == '':
|
||||
# set form fields
|
||||
fields = []
|
||||
for i in range( len(self.current_form['fields']) ):
|
||||
fields.append(self.__get_field(i, **kwd))
|
||||
# get the user entered fields
|
||||
index = 0
|
||||
while True:
|
||||
if params.get( 'field_name_%i' % index, False ):
|
||||
fields.append( self.__get_field( index, **kwd ) )
|
||||
index = index + 1
|
||||
else:
|
||||
break
|
||||
fields = fields
|
||||
else:
|
||||
fields, layout = self.__import_fields(trans, csv_file, form_type)
|
||||
return name, desc, form_type, layout, fields
|
||||
def __update_current_form(self, trans, **kwd):
|
||||
name, desc, form_type, layout, fields = self.__get_form(trans, **kwd)
|
||||
self.current_form = {}
|
||||
self.current_form['name'] = name
|
||||
self.current_form['desc'] = desc
|
||||
self.current_form['type'] = form_type
|
||||
self.current_form['layout'] = layout
|
||||
self.current_form['fields'] = fields
|
||||
return dict(name = name,
|
||||
desc = desc,
|
||||
type = form_type,
|
||||
layout = layout,
|
||||
fields = fields)
|
||||
|
||||
def __import_fields(self, trans, csv_file, form_type):
|
||||
'''
|
||||
@@ -356,7 +408,20 @@ class Forms( BaseController ):
|
||||
**kwd))
|
||||
self.__imported_from_file = True
|
||||
return fields, list(layouts)
|
||||
|
||||
def __validate_form(self, **kwd):
|
||||
'''
|
||||
This method checks the following text inputs are filled out by the user
|
||||
- the name of form
|
||||
- form type
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
# form name
|
||||
if not util.restore_text( params.name ):
|
||||
return None, 'Form name must be filled.'
|
||||
# form type
|
||||
if util.restore_text( params.form_type_selectbox ) == 'none':
|
||||
return None, 'Form type must be selected.'
|
||||
return True, ''
|
||||
def __save_form(self, trans, fdc_id=None, **kwd):
|
||||
'''
|
||||
This method saves the current form
|
||||
@@ -365,13 +430,18 @@ class Forms( BaseController ):
|
||||
flag, msg = self.__validate_form(**kwd)
|
||||
if not flag:
|
||||
return None, msg
|
||||
name, desc, form_type, layout, fields = self.__get_form(trans, **kwd)
|
||||
current_form = self.__get_form( trans, **kwd )
|
||||
# validate fields
|
||||
for field in fields:
|
||||
for field in current_form[ 'fields' ]:
|
||||
if not field[ 'label' ]:
|
||||
return None, "All the field label(s) must be completed."
|
||||
fd = trans.app.model.FormDefinition(name, desc, fields, current_form=None,
|
||||
form_type=form_type, layout=layout )
|
||||
# create a new form definition
|
||||
fd = trans.app.model.FormDefinition(name=current_form[ 'name' ],
|
||||
desc=current_form[ 'desc' ],
|
||||
fields=current_form[ 'fields' ],
|
||||
form_definition_current=None,
|
||||
form_type=current_form[ 'type' ],
|
||||
layout=current_form[ 'layout' ] )
|
||||
if fdc_id: # save changes to the existing form
|
||||
# change the pointer in the form_definition_current table to point
|
||||
# to this new record
|
||||
@@ -467,7 +537,7 @@ class Forms( BaseController ):
|
||||
def label(self):
|
||||
return str(self.index)+'.'+self.label
|
||||
|
||||
def __show( self, trans, form, msg='', messagetype='done', **kwd ):
|
||||
def __show( self, trans, form, current_form, msg='', messagetype='done', **kwd ):
|
||||
'''
|
||||
This method displays the form and any of the changes made to it,
|
||||
The empty_form param allows for this method to simulate clicking
|
||||
@@ -476,18 +546,18 @@ class Forms( BaseController ):
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
# name & description
|
||||
form_details = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ),
|
||||
( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ),
|
||||
( 'Type', self.__form_types_widget(trans, selected=self.current_form['type']) ) ]
|
||||
form_details = [ ( 'Name', TextField( 'name', 40, current_form[ 'name' ] ) ),
|
||||
( 'Description', TextField( 'description', 40, current_form[ 'desc' ] ) ),
|
||||
( 'Type', self.__form_types_widget(trans, selected=current_form[ 'type' ]) ) ]
|
||||
form_layout = []
|
||||
if self.current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE:
|
||||
for index, lg in enumerate(self.current_form['layout']):
|
||||
if current_form[ 'type' ] == trans.app.model.FormDefinition.types.SAMPLE:
|
||||
for index, lg in enumerate(current_form[ 'layout' ]):
|
||||
form_layout.append( TextField( 'grid_layout%i' % index, 40, lg ))
|
||||
# fields
|
||||
field_details = []
|
||||
for index, field in enumerate( self.current_form[ 'fields' ] ):
|
||||
if self.current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE:
|
||||
field_ui = self.FieldUI( self.current_form['layout'], index, field )
|
||||
for index, field in enumerate( current_form[ 'fields' ] ):
|
||||
if current_form['type'] == trans.app.model.FormDefinition.types.SAMPLE:
|
||||
field_ui = self.FieldUI( current_form['layout'], index, field )
|
||||
else:
|
||||
field_ui = self.FieldUI( None, index, field )
|
||||
field_details.append( field_ui.get() )
|
||||
@@ -498,7 +568,7 @@ class Forms( BaseController ):
|
||||
field_types=BaseField.form_field_types(),
|
||||
msg=msg,
|
||||
messagetype=messagetype,
|
||||
current_form_type=self.current_form['type'],
|
||||
current_form_type=current_form[ 'type' ],
|
||||
layout_grids=form_layout )
|
||||
|
||||
# Common methods for all components that use forms
|
||||
|
||||
@@ -115,20 +115,17 @@ class Requests( BaseController ):
|
||||
status='error',
|
||||
message="Invalid request ID",
|
||||
**kwd) )
|
||||
self.current_samples = []
|
||||
self.edit_mode = False
|
||||
current_samples = []
|
||||
for s in request.samples:
|
||||
self.current_samples.append([s.name, s.values.content])
|
||||
current_samples.append([s.name, s.values.content])
|
||||
if add_sample:
|
||||
self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]])
|
||||
self.details_state = 'Show request details'
|
||||
current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, id),
|
||||
current_samples = self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details='hide', edit_mode='False')
|
||||
def request_details(self, trans, id):
|
||||
'''
|
||||
Shows the request details
|
||||
@@ -186,25 +183,34 @@ class Requests( BaseController ):
|
||||
value=request.values.content[index],
|
||||
helptext=field['helptext']+' ('+req+')'))
|
||||
return request_details
|
||||
|
||||
def __update_samples(self, request, **kwd):
|
||||
'''
|
||||
This method retrieves all the user entered sample information and
|
||||
returns an list of all the samples and their field values
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
num_samples = len(self.current_samples)
|
||||
self.current_samples = []
|
||||
current_samples = []
|
||||
for s in request.samples:
|
||||
self.current_samples.append([s.name, s.values.content])
|
||||
for index in range(num_samples-len(request.samples)):
|
||||
sample_index = index + len(request.samples)
|
||||
sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
for field_index in range(len(request.type.sample_form.fields)):
|
||||
sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
|
||||
self.current_samples.append([sample_name, sample_values])
|
||||
|
||||
def __copy_sample(self):
|
||||
current_samples.append([s.name, s.values.content])
|
||||
index = len(request.samples)
|
||||
while True:
|
||||
if params.get( 'sample_%i_name' % index, '' ):
|
||||
sample_index = index
|
||||
sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
for field_index in range(len(request.type.sample_form.fields)):
|
||||
sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
|
||||
current_samples.append([sample_name, sample_values])
|
||||
index = index + 1
|
||||
else:
|
||||
break
|
||||
details = params.get( 'details', 'hide' )
|
||||
edit_mode = params.get( 'edit_mode', 'False' )
|
||||
return current_samples, details, edit_mode
|
||||
def __copy_sample(self, current_samples):
|
||||
copy_list = SelectField('copy_sample')
|
||||
copy_list.add_option('None', -1, selected=True)
|
||||
for i, s in enumerate(self.current_samples):
|
||||
for i, s in enumerate(current_samples):
|
||||
copy_list.add_option(s[0], i)
|
||||
return copy_list
|
||||
@web.expose
|
||||
@@ -221,20 +227,22 @@ class Requests( BaseController ):
|
||||
status='error',
|
||||
message="Invalid request ID",
|
||||
**kwd) )
|
||||
# get the user entered sample details
|
||||
current_samples, details, edit_mode = self.__update_samples( request, **kwd )
|
||||
if params.get('import_samples_button', False) == 'Import samples':
|
||||
try:
|
||||
file_obj = params.get('file_data', '')
|
||||
import csv
|
||||
reader = csv.reader(file_obj.file)
|
||||
for row in reader:
|
||||
self.current_samples.append([row[0], row[1:]])
|
||||
current_samples.append([row[0], row[1:]])
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
current_samples=current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
@@ -242,39 +250,35 @@ class Requests( BaseController ):
|
||||
message='Error in importing samples file',
|
||||
**kwd))
|
||||
elif params.get('add_sample_button', False) == 'Add New':
|
||||
# save the all (saved+unsaved) sample info in 'current_samples'
|
||||
self.__update_samples(request, **kwd)
|
||||
# add an empty or filled sample
|
||||
# if the user has selected a sample no. to copy then copy the contents
|
||||
# of the src sample to the new sample else an empty sample
|
||||
src_sample_index = int(params.get( 'copy_sample', -1 ))
|
||||
if src_sample_index == -1:
|
||||
# empty sample
|
||||
self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]])
|
||||
current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
|
||||
else:
|
||||
self.current_samples.append([self.current_samples[src_sample_index][0]+'_%i' % (len(self.current_samples)+1),
|
||||
[val for val in self.current_samples[src_sample_index][1]]])
|
||||
current_samples.append([current_samples[src_sample_index][0]+'_%i' % (len(current_samples)+1),
|
||||
[val for val in current_samples[src_sample_index][1]]])
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
current_samples=current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
elif params.get('save_samples_button', False) == 'Save':
|
||||
# update current_samples
|
||||
self.__update_samples(request, **kwd)
|
||||
# check for duplicate sample names
|
||||
msg = ''
|
||||
for index in range(len(self.current_samples)-len(request.samples)):
|
||||
for index in range(len(current_samples)-len(request.samples)):
|
||||
sample_index = index + len(request.samples)
|
||||
sample_name = self.current_samples[sample_index][0]
|
||||
sample_name = current_samples[sample_index][0]
|
||||
if not sample_name.strip():
|
||||
msg = 'Please enter the name of sample number %i' % sample_index
|
||||
break
|
||||
count = 0
|
||||
for i in range(len(self.current_samples)):
|
||||
if sample_name == self.current_samples[i][0]:
|
||||
for i in range(len(current_samples)):
|
||||
if sample_name == current_samples[i][0]:
|
||||
count = count + 1
|
||||
if count > 1:
|
||||
msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
|
||||
@@ -283,12 +287,13 @@ class Requests( BaseController ):
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = self.current_samples,
|
||||
sample_copy=self.__copy_sample(), details_state=self.details_state,
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details, edit_mode=edit_mode,
|
||||
messagetype='error', msg=msg)
|
||||
# save all the new/unsaved samples entered by the user
|
||||
if not self.edit_mode:
|
||||
for index in range(len(self.current_samples)-len(request.samples)):
|
||||
if edit_mode == 'False':
|
||||
for index in range(len(current_samples)-len(request.samples)):
|
||||
sample_index = index + len(request.samples)
|
||||
sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
@@ -299,9 +304,9 @@ class Requests( BaseController ):
|
||||
s = trans.app.model.Sample(sample_name, '', request, form_values)
|
||||
s.flush()
|
||||
else:
|
||||
for index in range(len(self.current_samples)):
|
||||
for index in range(len(current_samples)):
|
||||
sample_index = index
|
||||
sample_name = self.current_samples[sample_index][0]
|
||||
sample_name = current_samples[sample_index][0]
|
||||
new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
for field_index in range(len(request.type.sample_form.fields)):
|
||||
@@ -318,14 +323,14 @@ class Requests( BaseController ):
|
||||
operation='show_request',
|
||||
id=trans.security.encode_id(request.id)) )
|
||||
elif params.get('edit_samples_button', False) == 'Edit samples':
|
||||
self.edit_mode = True
|
||||
edit_mode = 'True'
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
current_samples=current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
elif params.get('cancel_changes_button', False) == 'Cancel':
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
@@ -340,21 +345,22 @@ class Requests( BaseController ):
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', 0)))
|
||||
current_samples, details, edit_mode = self.__update_samples( request, **kwd )
|
||||
sample_index = int(params.get('sample_id', 0))
|
||||
sample_name = self.current_samples[sample_index][0]
|
||||
sample_name = current_samples[sample_index][0]
|
||||
s = request.has_sample(sample_name)
|
||||
if s:
|
||||
s.delete()
|
||||
s.flush()
|
||||
request.flush()
|
||||
del self.current_samples[sample_index]
|
||||
del current_samples[sample_index]
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
|
||||
@web.expose
|
||||
@web.require_login( "create/submit sequencing requests" )
|
||||
@@ -363,17 +369,14 @@ class Requests( BaseController ):
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', 0)))
|
||||
if self.details_state == 'Show request details':
|
||||
self.details_state = 'Hide request details'
|
||||
elif self.details_state == 'Hide request details':
|
||||
self.details_state = 'Show request details'
|
||||
current_samples, details, edit_mode = self.__update_samples( request, **kwd )
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
def __select_request_type(self, trans, rtid):
|
||||
rt_ids = ['none']
|
||||
for rt in trans.app.model.RequestType.query().all():
|
||||
@@ -476,17 +479,22 @@ class Requests( BaseController ):
|
||||
msg=msg,
|
||||
messagetype=messagetype)
|
||||
def __library_ui(self, trans, request=None, **kwd):
|
||||
'''
|
||||
This method creates the data library & folder selectbox for new &
|
||||
editing requests. First we get a list of all the libraries accessible to
|
||||
the current user and display it in a selectbox. If the user has select an
|
||||
existing library then display all the accessible sub folders of the selected
|
||||
data library.
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
lib_id = params.get( 'library_id', 'none' )
|
||||
# if editing a request
|
||||
selected_lib = None
|
||||
# if editing a request and the user has already associated a library to
|
||||
# this request, then set the selected_lib to the request.library
|
||||
if request and lib_id == 'none':
|
||||
if request.library:
|
||||
lib_id = str(request.library.id)
|
||||
selected_lib = request.library
|
||||
else:
|
||||
# new request
|
||||
selected_lib = None
|
||||
# get all permitted libraries for this user
|
||||
all_libraries = trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted == False ) \
|
||||
.order_by( trans.app.model.Library.name ).all()
|
||||
@@ -497,15 +505,16 @@ class Requests( BaseController ):
|
||||
can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check )
|
||||
if can_show:
|
||||
libraries[ library ] = hidden_folder_ids
|
||||
# create data library selectbox with refresh on change enabled
|
||||
lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
|
||||
lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list )
|
||||
# fill up the options in the Library selectfield
|
||||
# first option
|
||||
# fill up the options in the Library selectbox
|
||||
# first option 'none' is the value for "Select one" option
|
||||
if lib_id == 'none':
|
||||
lib_list.add_option('Select one', 'none', selected=True)
|
||||
else:
|
||||
lib_list.add_option('Select one', 'none')
|
||||
# all the libraries available to the user
|
||||
# add all the libraries available to the user to the library selectbox
|
||||
for lib, hidden_folder_ids in libraries.items():
|
||||
if str(lib.id) == lib_id:
|
||||
lib_list.add_option(lib.name, lib.id, selected=True)
|
||||
@@ -524,14 +533,21 @@ class Requests( BaseController ):
|
||||
helptext='Data library where the resultant dataset will be stored.')
|
||||
# show the folder widget only if the user has selected a valid library above
|
||||
if selected_lib:
|
||||
# when editing a request
|
||||
# when editing a request, either the user has already selected a subfolder or not
|
||||
if request:
|
||||
if request.folder:
|
||||
current_fid = request.folder.id
|
||||
else:
|
||||
current_fid = request.library.root_folder.id
|
||||
else:
|
||||
# when a folder not yet associated with the request then the
|
||||
# the current folder is set to the root_folder of the
|
||||
# parent data library if present.
|
||||
if request.library:
|
||||
current_fid = request.library.root_folder.id
|
||||
else:
|
||||
current_fid = params.get( 'folder_id', 'none' )
|
||||
else:
|
||||
current_fid = params.get( 'folder_id', 'none' )
|
||||
# create the folder selectbox
|
||||
folder_list = SelectField( 'folder_id')
|
||||
# first option
|
||||
if lib_id == 'none':
|
||||
@@ -543,6 +559,7 @@ class Requests( BaseController ):
|
||||
selected_lib,
|
||||
actions_to_check,
|
||||
selected_hidden_folder_ids )
|
||||
# add all the folders to the folder selectbox
|
||||
for f in showable_folders:
|
||||
if str(f.id) == str(current_fid):
|
||||
folder_list.add_option(f.name, f.id, selected=True)
|
||||
@@ -568,8 +585,6 @@ class Requests( BaseController ):
|
||||
Validates the request entered by the user
|
||||
'''
|
||||
empty_fields = []
|
||||
# if not request.library:
|
||||
# empty_fields.append('Data library')
|
||||
# check rest of the fields of the form
|
||||
for index, field in enumerate(request.type.request_form.fields):
|
||||
if field['required'] == 'required' and request.values.content[index] in ['', None]:
|
||||
|
||||
@@ -11,6 +11,10 @@ from galaxy.web.controllers.forms import get_all_forms
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
#
|
||||
# ---- Request Grid ------------------------------------------------------------
|
||||
#
|
||||
|
||||
class RequestsListGrid( grids.Grid ):
|
||||
title = "Sequencing Requests"
|
||||
template = "admin/requests/grid.mako"
|
||||
@@ -60,6 +64,11 @@ class RequestsListGrid( grids.Grid ):
|
||||
else:
|
||||
return query
|
||||
|
||||
|
||||
#
|
||||
# ---- Request Controller ------------------------------------------------------
|
||||
#
|
||||
|
||||
class Requests( BaseController ):
|
||||
request_grid = RequestsListGrid()
|
||||
|
||||
@@ -67,6 +76,7 @@ class Requests( BaseController ):
|
||||
@web.require_admin
|
||||
def index( self, trans ):
|
||||
return trans.fill_template( "/admin/requests/index.mako" )
|
||||
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def list( self, trans, **kwargs ):
|
||||
@@ -104,51 +114,26 @@ class Requests( BaseController ):
|
||||
self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED)
|
||||
# Render the list view
|
||||
return self.request_grid( trans, **kwargs )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def edit(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
def __show_request(self, trans, id, messagetype, msg):
|
||||
try:
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', None)))
|
||||
request = trans.app.model.Request.get(id)
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
status='error',
|
||||
message="Invalid request ID",
|
||||
**kwd) )
|
||||
if params.get('show', False) == 'True':
|
||||
return self.__edit_request(trans, request.id, **kwd)
|
||||
elif params.get('save_changes_request_button', False) == 'Save changes' \
|
||||
or params.get('edit_samples_button', False) == 'Edit samples':
|
||||
request_type = trans.app.model.RequestType.get(int(params.select_request_type))
|
||||
if not util.restore_text(params.get('name', '')):
|
||||
msg = 'Please enter the <b>Name</b> of the request'
|
||||
kwd['messagetype'] = 'error'
|
||||
kwd['msg'] = msg
|
||||
kwd['show'] = 'True'
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='edit',
|
||||
**kwd) )
|
||||
request = self.__save_request(trans, request, **kwd)
|
||||
msg = 'The changes made to the request named %s has been saved' % request.name
|
||||
if params.get('save_changes_request_button', False) == 'Save changes':
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
message=msg ,
|
||||
status='done') )
|
||||
elif params.get('edit_samples_button', False) == 'Edit samples':
|
||||
new_kwd = {}
|
||||
new_kwd['request_id'] = request.id
|
||||
new_kwd['edit_samples_button'] = 'Edit samples'
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='show_request',
|
||||
msg=msg ,
|
||||
messagetype='done',
|
||||
**new_kwd) )
|
||||
elif params.get('refresh', False) == 'true':
|
||||
return self.__edit_request(trans, request.id, **kwd)
|
||||
current_samples = []
|
||||
for s in request.samples:
|
||||
current_samples.append([s.name, s.values.content])
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, id),
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details='hide', edit_mode='False',
|
||||
msg=msg, messagetype=messagetype)
|
||||
|
||||
def __edit_request(self, trans, id, **kwd):
|
||||
try:
|
||||
request = trans.app.model.Request.get(id)
|
||||
@@ -276,317 +261,10 @@ class Requests( BaseController ):
|
||||
action='list',
|
||||
show_filter=trans.app.model.Request.states.SUBMITTED,
|
||||
**kwd) )
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def submit_request(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
try:
|
||||
id = int(params.get('id', False))
|
||||
request = trans.app.model.Request.get(id)
|
||||
except:
|
||||
msg = "Invalid request ID"
|
||||
log.warn( msg )
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
status='error',
|
||||
message=msg,
|
||||
**kwd) )
|
||||
msg = self.__validate(trans, request)
|
||||
if msg:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='edit',
|
||||
messagetype='error',
|
||||
msg=msg,
|
||||
request_id=request.id,
|
||||
show='True') )
|
||||
# get the new state
|
||||
new_state = request.type.states[0]
|
||||
for s in request.samples:
|
||||
event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system')
|
||||
event.flush()
|
||||
# change request's submitted field
|
||||
request.state = request.states.SUBMITTED
|
||||
request.flush()
|
||||
kwd['id'] = trans.security.encode_id(request.id)
|
||||
kwd['status'] = 'done'
|
||||
kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
show_filter=trans.app.model.Request.states.SUBMITTED,
|
||||
**kwd) )
|
||||
def __copy_sample(self):
|
||||
copy_list = SelectField('copy_sample')
|
||||
copy_list.add_option('None', -1, selected=True)
|
||||
for i, s in enumerate(self.current_samples):
|
||||
copy_list.add_option(s[0], i)
|
||||
return copy_list
|
||||
def __update_samples(self, request, **kwd):
|
||||
params = util.Params( kwd )
|
||||
num_samples = len(self.current_samples)
|
||||
self.current_samples = []
|
||||
for s in request.samples:
|
||||
self.current_samples.append([s.name, s.values.content])
|
||||
for index in range(num_samples-len(request.samples)):
|
||||
sample_index = index + len(request.samples)
|
||||
sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
for field_index in range(len(request.type.sample_form.fields)):
|
||||
sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
|
||||
self.current_samples.append([sample_name, sample_values])
|
||||
def __show_request(self, trans, id, messagetype, msg):
|
||||
try:
|
||||
request = trans.app.model.Request.get(id)
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
status='error',
|
||||
message="Invalid request ID",
|
||||
**kwd) )
|
||||
self.current_samples = []
|
||||
self.edit_mode = False
|
||||
for s in request.samples:
|
||||
self.current_samples.append([s.name, s.values.content])
|
||||
self.details_state = 'Show request details'
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, id),
|
||||
current_samples = self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode,
|
||||
msg=msg, messagetype=messagetype)
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def show_request(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
try:
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', None)))
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
status='error',
|
||||
message="Invalid request ID",
|
||||
**kwd) )
|
||||
if params.get('import_samples_button', False) == 'Import samples':
|
||||
try:
|
||||
file_obj = params.get('file_data', '')
|
||||
import csv
|
||||
reader = csv.reader(file_obj.file)
|
||||
for row in reader:
|
||||
self.current_samples.append([row[0], row[1:]])
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
status='error',
|
||||
operation='show_request',
|
||||
id=trans.security.encode_id(request.id),
|
||||
message='Error in importing samples from the given file.',
|
||||
**kwd))
|
||||
elif params.get('add_sample_button', False) == 'Add New':
|
||||
# save the all (saved+unsaved) sample info in 'current_samples'
|
||||
self.__update_samples(request, **kwd)
|
||||
# add an empty or filled sample
|
||||
# if the user has selected a sample no. to copy then copy the contents
|
||||
# of the src sample to the new sample else an empty sample
|
||||
src_sample_index = int(params.get( 'copy_sample', -1 ))
|
||||
if src_sample_index == -1:
|
||||
# empty sample
|
||||
self.current_samples.append(['Sample_%i' % (len(self.current_samples)+1),['' for field in request.type.sample_form.fields]])
|
||||
else:
|
||||
self.current_samples.append([self.current_samples[src_sample_index][0]+'_%i' % (len(self.current_samples)+1),
|
||||
[val for val in self.current_samples[src_sample_index][1]]])
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
elif params.get('save_samples_button', False) == 'Save':
|
||||
# update current_samples
|
||||
self.__update_samples(request, **kwd)
|
||||
# check for duplicate sample names
|
||||
msg = ''
|
||||
for index in range(len(self.current_samples)-len(request.samples)):
|
||||
sample_index = index + len(request.samples)
|
||||
sample_name = self.current_samples[sample_index][0]
|
||||
if not sample_name.strip():
|
||||
msg = 'Please enter the name of sample number %i' % sample_index
|
||||
break
|
||||
count = 0
|
||||
for i in range(len(self.current_samples)):
|
||||
if sample_name == self.current_samples[i][0]:
|
||||
count = count + 1
|
||||
if count > 1:
|
||||
msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
|
||||
break
|
||||
if msg:
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = self.current_samples,
|
||||
sample_copy=self.__copy_sample(), details_state=self.details_state,
|
||||
messagetype='error', msg=msg)
|
||||
# save all the new/unsaved samples entered by the user
|
||||
if not self.edit_mode:
|
||||
for index in range(len(self.current_samples)-len(request.samples)):
|
||||
sample_index = index + len(request.samples)
|
||||
sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
for field_index in range(len(request.type.sample_form.fields)):
|
||||
sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
|
||||
form_values = trans.app.model.FormValues(request.type.sample_form, sample_values)
|
||||
form_values.flush()
|
||||
s = trans.app.model.Sample(sample_name, '', request, form_values)
|
||||
s.flush()
|
||||
else:
|
||||
for index in range(len(self.current_samples)):
|
||||
sample_index = index
|
||||
sample_name = self.current_samples[sample_index][0]
|
||||
new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
for field_index in range(len(request.type.sample_form.fields)):
|
||||
sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
|
||||
sample = request.has_sample(sample_name)
|
||||
if sample:
|
||||
form_values = trans.app.model.FormValues.get(sample.values.id)
|
||||
form_values.content = sample_values
|
||||
form_values.flush()
|
||||
sample.name = new_sample_name
|
||||
sample.flush()
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
operation='show_request',
|
||||
id=trans.security.encode_id(request.id)) )
|
||||
elif params.get('edit_samples_button', False) == 'Edit samples':
|
||||
self.edit_mode = True
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
elif params.get('cancel_changes_button', False) == 'Cancel':
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
operation='show_request',
|
||||
id=trans.security.encode_id(request.id)) )
|
||||
|
||||
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def delete_sample(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', 0)))
|
||||
sample_index = int(params.get('sample_id', 0))
|
||||
sample_name = self.current_samples[sample_index][0]
|
||||
s = request.has_sample(sample_name)
|
||||
if s:
|
||||
s.delete()
|
||||
s.flush()
|
||||
request.flush()
|
||||
del self.current_samples[sample_index]
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = self.current_samples,
|
||||
sample_copy=self.__copy_sample(),
|
||||
details_state=self.details_state,
|
||||
edit_mode=self.edit_mode)
|
||||
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def toggle_request_details(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', 0)))
|
||||
if self.details_state == 'Show request details':
|
||||
self.details_state = 'Hide request details'
|
||||
elif self.details_state == 'Hide request details':
|
||||
self.details_state = 'Show request details'
|
||||
copy_list = SelectField('copy_sample')
|
||||
copy_list.add_option('None', -1, selected=True)
|
||||
for i, s in enumerate(self.current_samples):
|
||||
copy_list.add_option(i+1, i)
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = self.current_samples,
|
||||
sample_copy=copy_list, details_state=self.details_state)
|
||||
def request_details(self, trans, id):
|
||||
'''
|
||||
Shows the request details
|
||||
'''
|
||||
request = trans.app.model.Request.get(id)
|
||||
# list of widgets to be rendered on the request form
|
||||
request_details = []
|
||||
# main details
|
||||
request_details.append(dict(label='User',
|
||||
value=str(request.user.email),
|
||||
helptext=''))
|
||||
request_details.append(dict(label='Description',
|
||||
value=request.desc,
|
||||
helptext=''))
|
||||
request_details.append(dict(label='Type',
|
||||
value=request.type.name,
|
||||
helptext=''))
|
||||
request_details.append(dict(label='State',
|
||||
value=request.state,
|
||||
helptext=''))
|
||||
request_details.append(dict(label='Date created',
|
||||
value=request.create_time,
|
||||
helptext=''))
|
||||
# library associated
|
||||
if request.library:
|
||||
value=request.library.name
|
||||
else:
|
||||
value = None
|
||||
request_details.append(dict(label='Data library',
|
||||
value=value,
|
||||
helptext='Data library where the resultant dataset will be stored'))
|
||||
# folder associated
|
||||
if request.folder:
|
||||
value = request.folder.name
|
||||
else:
|
||||
value = None
|
||||
request_details.append( dict( label='Data library folder',
|
||||
value=value,
|
||||
helptext='Data library folder where the resultant dataset will be stored' ) )
|
||||
|
||||
# form fields
|
||||
for index, field in enumerate(request.type.request_form.fields):
|
||||
if field['required']:
|
||||
req = 'Required'
|
||||
else:
|
||||
req = 'Optional'
|
||||
if field['type'] == 'AddressField':
|
||||
if request.values.content[index]:
|
||||
request_details.append(dict(label=field['label'],
|
||||
value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(),
|
||||
helptext=field['helptext']+' ('+req+')'))
|
||||
else:
|
||||
request_details.append(dict(label=field['label'],
|
||||
value=None,
|
||||
helptext=field['helptext']+' ('+req+')'))
|
||||
else:
|
||||
request_details.append(dict(label=field['label'],
|
||||
value=request.values.content[index],
|
||||
helptext=field['helptext']+' ('+req+')'))
|
||||
return request_details
|
||||
|
||||
#
|
||||
#---- Request Creation ----------------------------------------------------------
|
||||
#
|
||||
def __select_request_type(self, trans, rtid):
|
||||
rt_ids = ['none']
|
||||
for rt in trans.app.model.RequestType.query().all():
|
||||
@@ -723,21 +401,22 @@ class Requests( BaseController ):
|
||||
return select_user
|
||||
|
||||
def __library_ui(self, trans, user, request=None, **kwd):
|
||||
"""
|
||||
Return a list of libraries for which user has the permission
|
||||
to perform the LIBRARY_ADD action on any of it's folders
|
||||
"""
|
||||
'''
|
||||
This method creates the data library & folder selectbox for new &
|
||||
editing requests. First we get a list of all the libraries accessible to
|
||||
the current user and display it in a selectbox. If the user has select an
|
||||
existing library then display all the accessible sub folders of the selected
|
||||
data library.
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
lib_id = params.get( 'library_id', 'none' )
|
||||
# if editing a request
|
||||
# if editing a request and the user has already associated a library to
|
||||
# this request, then set the selected_lib to the request.library
|
||||
selected_lib = None
|
||||
if request and lib_id == 'none':
|
||||
if request.library:
|
||||
lib_id = str(request.library.id)
|
||||
selected_lib = request.library
|
||||
else:
|
||||
# new request
|
||||
selected_lib = None
|
||||
# if new request no user is selected initially, none of the libraries are
|
||||
# listed in the selectfield
|
||||
if not user:
|
||||
@@ -759,10 +438,11 @@ class Requests( BaseController ):
|
||||
can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check )
|
||||
if can_show:
|
||||
libraries[ library ] = hidden_folder_ids
|
||||
# create the selectfield
|
||||
# create data library selectbox with refresh on change enabled
|
||||
lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
|
||||
lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list )
|
||||
# first option
|
||||
# fill up the options in the Library selectbox
|
||||
# first option 'none' is the value for "Select one" option
|
||||
if lib_id == 'none':
|
||||
lib_list.add_option('Select one', 'none', selected=True)
|
||||
else:
|
||||
@@ -784,15 +464,23 @@ class Requests( BaseController ):
|
||||
lib_widget = dict(label='Data library',
|
||||
widget=lib_list,
|
||||
helptext='Data library where the resultant dataset will be stored.')
|
||||
# show the folder widget only if the user has selected a valid library above
|
||||
if selected_lib:
|
||||
# when editing a request
|
||||
# when editing a request, either the user has already selected a subfolder or not
|
||||
if request:
|
||||
if request.folder:
|
||||
current_fid = request.folder.id
|
||||
else:
|
||||
current_fid = request.library.root_folder.id
|
||||
else:
|
||||
# when a folder not yet associated with the request then the
|
||||
# the current folder is set to the root_folder of the
|
||||
# parent data library if present.
|
||||
if request.library:
|
||||
current_fid = request.library.root_folder.id
|
||||
else:
|
||||
current_fid = params.get( 'folder_id', 'none' )
|
||||
else:
|
||||
current_fid = params.get( 'folder_id', 'none' )
|
||||
# create the folder selectbox
|
||||
folder_list = SelectField( 'folder_id')
|
||||
# first option
|
||||
if lib_id == 'none':
|
||||
@@ -828,9 +516,14 @@ class Requests( BaseController ):
|
||||
'''
|
||||
Validates the request entered by the user
|
||||
'''
|
||||
if not request.samples:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
operation='show_request',
|
||||
message='Please add one or more samples to this request before submitting.',
|
||||
status='error',
|
||||
id=trans.security.encode_id(request.id)) )
|
||||
empty_fields = []
|
||||
# if not request.library:
|
||||
# empty_fields.append('Library')
|
||||
# check rest of the fields of the form
|
||||
for index, field in enumerate(request.type.request_form.fields):
|
||||
if field['required'] == 'required' and request.values.content[index] in ['', None]:
|
||||
@@ -909,6 +602,350 @@ class Requests( BaseController ):
|
||||
request.folder = folder
|
||||
request.flush()
|
||||
return request
|
||||
|
||||
|
||||
#
|
||||
#---- Request Editing ----------------------------------------------------------
|
||||
#
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def edit(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
try:
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', None)))
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
status='error',
|
||||
message="Invalid request ID",
|
||||
**kwd) )
|
||||
if params.get('show', False) == 'True':
|
||||
return self.__edit_request(trans, request.id, **kwd)
|
||||
elif params.get('save_changes_request_button', False) == 'Save changes' \
|
||||
or params.get('edit_samples_button', False) == 'Edit samples':
|
||||
request_type = trans.app.model.RequestType.get(int(params.select_request_type))
|
||||
if not util.restore_text(params.get('name', '')):
|
||||
msg = 'Please enter the <b>Name</b> of the request'
|
||||
kwd['messagetype'] = 'error'
|
||||
kwd['msg'] = msg
|
||||
kwd['show'] = 'True'
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='edit',
|
||||
**kwd) )
|
||||
request = self.__save_request(trans, request, **kwd)
|
||||
msg = 'The changes made to the request named %s has been saved' % request.name
|
||||
if params.get('save_changes_request_button', False) == 'Save changes':
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
message=msg ,
|
||||
status='done') )
|
||||
elif params.get('edit_samples_button', False) == 'Edit samples':
|
||||
new_kwd = {}
|
||||
new_kwd['request_id'] = request.id
|
||||
new_kwd['edit_samples_button'] = 'Edit samples'
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='show_request',
|
||||
msg=msg ,
|
||||
messagetype='done',
|
||||
**new_kwd) )
|
||||
elif params.get('refresh', False) == 'true':
|
||||
return self.__edit_request(trans, request.id, **kwd)
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def submit_request(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
try:
|
||||
id = int(params.get('id', False))
|
||||
request = trans.app.model.Request.get(id)
|
||||
except:
|
||||
msg = "Invalid request ID"
|
||||
log.warn( msg )
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
status='error',
|
||||
message=msg,
|
||||
**kwd) )
|
||||
msg = self.__validate(trans, request)
|
||||
if msg:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='edit',
|
||||
messagetype='error',
|
||||
msg=msg,
|
||||
request_id=request.id,
|
||||
show='True') )
|
||||
# get the new state
|
||||
new_state = request.type.states[0]
|
||||
for s in request.samples:
|
||||
event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system')
|
||||
event.flush()
|
||||
# change request's submitted field
|
||||
request.state = request.states.SUBMITTED
|
||||
request.flush()
|
||||
kwd['id'] = trans.security.encode_id(request.id)
|
||||
kwd['status'] = 'done'
|
||||
kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
show_filter=trans.app.model.Request.states.SUBMITTED,
|
||||
**kwd) )
|
||||
def __update_samples(self, request, **kwd):
|
||||
'''
|
||||
This method retrieves all the user entered sample information and
|
||||
returns an list of all the samples and their field values
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
current_samples = []
|
||||
for s in request.samples:
|
||||
current_samples.append([s.name, s.values.content])
|
||||
index = len(request.samples)
|
||||
while True:
|
||||
if params.get( 'sample_%i_name' % index, '' ):
|
||||
sample_index = index
|
||||
sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
for field_index in range(len(request.type.sample_form.fields)):
|
||||
sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
|
||||
current_samples.append([sample_name, sample_values])
|
||||
index = index + 1
|
||||
else:
|
||||
break
|
||||
details = params.get( 'details', 'hide' )
|
||||
edit_mode = params.get( 'edit_mode', 'False' )
|
||||
return current_samples, details, edit_mode
|
||||
def __copy_sample(self, current_samples):
|
||||
copy_list = SelectField('copy_sample')
|
||||
copy_list.add_option('None', -1, selected=True)
|
||||
for i, s in enumerate(current_samples):
|
||||
copy_list.add_option(s[0], i)
|
||||
return copy_list
|
||||
@web.expose
|
||||
@web.require_login( "create/submit sequencing requests" )
|
||||
def show_request(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
try:
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', None)))
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
status='error',
|
||||
message="Invalid request ID",
|
||||
**kwd) )
|
||||
# get the user entered sample details
|
||||
current_samples, details, edit_mode = self.__update_samples( request, **kwd )
|
||||
if params.get('import_samples_button', False) == 'Import samples':
|
||||
try:
|
||||
file_obj = params.get('file_data', '')
|
||||
import csv
|
||||
reader = csv.reader(file_obj.file)
|
||||
for row in reader:
|
||||
current_samples.append([row[0], row[1:]])
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
status='error',
|
||||
message='Error in importing samples file',
|
||||
**kwd))
|
||||
elif params.get('add_sample_button', False) == 'Add New':
|
||||
# add an empty or filled sample
|
||||
# if the user has selected a sample no. to copy then copy the contents
|
||||
# of the src sample to the new sample else an empty sample
|
||||
src_sample_index = int(params.get( 'copy_sample', -1 ))
|
||||
if src_sample_index == -1:
|
||||
# empty sample
|
||||
current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
|
||||
else:
|
||||
current_samples.append([current_samples[src_sample_index][0]+'_%i' % (len(current_samples)+1),
|
||||
[val for val in current_samples[src_sample_index][1]]])
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
elif params.get('save_samples_button', False) == 'Save':
|
||||
# check for duplicate sample names
|
||||
msg = ''
|
||||
for index in range(len(current_samples)-len(request.samples)):
|
||||
sample_index = index + len(request.samples)
|
||||
sample_name = current_samples[sample_index][0]
|
||||
if not sample_name.strip():
|
||||
msg = 'Please enter the name of sample number %i' % sample_index
|
||||
break
|
||||
count = 0
|
||||
for i in range(len(current_samples)):
|
||||
if sample_name == current_samples[i][0]:
|
||||
count = count + 1
|
||||
if count > 1:
|
||||
msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
|
||||
break
|
||||
if msg:
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details, edit_mode=edit_mode,
|
||||
messagetype='error', msg=msg)
|
||||
# save all the new/unsaved samples entered by the user
|
||||
if edit_mode == 'False':
|
||||
for index in range(len(current_samples)-len(request.samples)):
|
||||
sample_index = index + len(request.samples)
|
||||
sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
for field_index in range(len(request.type.sample_form.fields)):
|
||||
sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
|
||||
form_values = trans.app.model.FormValues(request.type.sample_form, sample_values)
|
||||
form_values.flush()
|
||||
s = trans.app.model.Sample(sample_name, '', request, form_values)
|
||||
s.flush()
|
||||
else:
|
||||
for index in range(len(current_samples)):
|
||||
sample_index = index
|
||||
sample_name = current_samples[sample_index][0]
|
||||
new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) )
|
||||
sample_values = []
|
||||
for field_index in range(len(request.type.sample_form.fields)):
|
||||
sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
|
||||
sample = request.has_sample(sample_name)
|
||||
if sample:
|
||||
form_values = trans.app.model.FormValues.get(sample.values.id)
|
||||
form_values.content = sample_values
|
||||
form_values.flush()
|
||||
sample.name = new_sample_name
|
||||
sample.flush()
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
operation='show_request',
|
||||
id=trans.security.encode_id(request.id)) )
|
||||
elif params.get('edit_samples_button', False) == 'Edit samples':
|
||||
edit_mode = 'True'
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
elif params.get('cancel_changes_button', False) == 'Cancel':
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='list',
|
||||
operation='show_request',
|
||||
id=trans.security.encode_id(request.id)) )
|
||||
|
||||
|
||||
@web.expose
|
||||
@web.require_login( "create/submit sequencing requests" )
|
||||
def delete_sample(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', 0)))
|
||||
current_samples, details, edit_mode = self.__update_samples( request, **kwd )
|
||||
sample_index = int(params.get('sample_id', 0))
|
||||
sample_name = current_samples[sample_index][0]
|
||||
s = request.has_sample(sample_name)
|
||||
if s:
|
||||
s.delete()
|
||||
s.flush()
|
||||
request.flush()
|
||||
del current_samples[sample_index]
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
|
||||
@web.expose
|
||||
@web.require_login( "create/submit sequencing requests" )
|
||||
def toggle_request_details(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
msg = util.restore_text( params.get( 'msg', '' ) )
|
||||
messagetype = params.get( 'messagetype', 'done' )
|
||||
request = trans.app.model.Request.get(int(params.get('request_id', 0)))
|
||||
current_samples, details, edit_mode = self.__update_samples( request, **kwd )
|
||||
return trans.fill_template( '/admin/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def request_details(self, trans, id):
|
||||
'''
|
||||
Shows the request details
|
||||
'''
|
||||
request = trans.app.model.Request.get(id)
|
||||
# list of widgets to be rendered on the request form
|
||||
request_details = []
|
||||
# main details
|
||||
request_details.append(dict(label='User',
|
||||
value=str(request.user.email),
|
||||
helptext=''))
|
||||
request_details.append(dict(label='Description',
|
||||
value=request.desc,
|
||||
helptext=''))
|
||||
request_details.append(dict(label='Type',
|
||||
value=request.type.name,
|
||||
helptext=''))
|
||||
request_details.append(dict(label='State',
|
||||
value=request.state,
|
||||
helptext=''))
|
||||
request_details.append(dict(label='Date created',
|
||||
value=request.create_time,
|
||||
helptext=''))
|
||||
# library associated
|
||||
if request.library:
|
||||
value=request.library.name
|
||||
else:
|
||||
value = None
|
||||
request_details.append(dict(label='Data library',
|
||||
value=value,
|
||||
helptext='Data library where the resultant dataset will be stored'))
|
||||
# folder associated
|
||||
if request.folder:
|
||||
value = request.folder.name
|
||||
else:
|
||||
value = None
|
||||
request_details.append( dict( label='Data library folder',
|
||||
value=value,
|
||||
helptext='Data library folder where the resultant dataset will be stored' ) )
|
||||
|
||||
# form fields
|
||||
for index, field in enumerate(request.type.request_form.fields):
|
||||
if field['required']:
|
||||
req = 'Required'
|
||||
else:
|
||||
req = 'Optional'
|
||||
if field['type'] == 'AddressField':
|
||||
if request.values.content[index]:
|
||||
request_details.append(dict(label=field['label'],
|
||||
value=trans.app.model.UserAddress.get(int(request.values.content[index])).get_html(),
|
||||
helptext=field['helptext']+' ('+req+')'))
|
||||
else:
|
||||
request_details.append(dict(label=field['label'],
|
||||
value=None,
|
||||
helptext=field['helptext']+' ('+req+')'))
|
||||
else:
|
||||
request_details.append(dict(label=field['label'],
|
||||
value=request.values.content[index],
|
||||
helptext=field['helptext']+' ('+req+')'))
|
||||
return request_details
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def bar_codes(self, trans, **kwd):
|
||||
@@ -1086,7 +1123,9 @@ class Requests( BaseController ):
|
||||
events_list=events_list,
|
||||
sample=sample, widgets=widgets, title=title)
|
||||
|
||||
# Request Type Stuff
|
||||
##
|
||||
#### Request Type Stuff ###################################################
|
||||
##
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def manage_request_types( self, trans, **kwd ):
|
||||
|
||||
@@ -635,7 +635,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
|
||||
return None
|
||||
|
||||
def request_types(self):
|
||||
if self.app.model.RequestType.query().all():
|
||||
if self.app.model.RequestType.query().filter_by(deleted=False).all():
|
||||
return True
|
||||
return False
|
||||
|
||||
|
||||
@@ -36,16 +36,20 @@ $( function() {
|
||||
<% options = field_attr[2] %>
|
||||
<div class="repeat-group-item">
|
||||
<div class="form-row">
|
||||
<label> Options</label>
|
||||
%for i, option in enumerate(options):
|
||||
<b> ${i+1}</b>
|
||||
${option[1].get_html()}
|
||||
<a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='remove', field_index=index, option_index=i )}">Remove</a><br>
|
||||
%endfor
|
||||
<label> Options</label>
|
||||
%for i, option in enumerate(options):
|
||||
<div class="form-row">
|
||||
<b> ${i+1}</b>
|
||||
${option[1].get_html()}
|
||||
##<a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='remove', field_index=index, option_index=i )}">Remove</a><br>
|
||||
<input type="submit" name="removeoption_${index}_${i}" value="Remove"/>
|
||||
</div>
|
||||
%endfor
|
||||
<input type="hidden" name="field_index" value="${index}"/>
|
||||
</div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form.id, select_box_options='add', field_index=index )}">Add</a>
|
||||
<input type="submit" name="addoption_${index}" value="Add"/>
|
||||
</div>
|
||||
%endif
|
||||
%endif
|
||||
@@ -81,7 +85,7 @@ $( function() {
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Edit form definition "${form.name}"</div>
|
||||
<form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id, num_fields=len(form.fields) )}" method="post" >
|
||||
<form id="edit_form" name="edit_form" action="${h.url_for( controller='forms', action='edit', form_id=form.id )}" method="post" >
|
||||
%for label, input in form_details:
|
||||
<div class="form-row">
|
||||
<label>${label}</label>
|
||||
|
||||
@@ -63,9 +63,19 @@
|
||||
|
||||
<div class="toolForm">
|
||||
%if form.desc:
|
||||
<div class="toolFormTitle">${form.name} - <i>${form.desc}</i></div>
|
||||
<div class="toolFormTitle">${form.name} - <i>${form.desc}</i>
|
||||
<a id="form-${form.id}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="form-${form.id}-popup">
|
||||
<a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit</a>
|
||||
</div>
|
||||
</div>
|
||||
%else:
|
||||
<div class="toolFormTitle">${form.name}</div>
|
||||
<div class="toolFormTitle">${form.name}
|
||||
<a id="form-${form.id}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="form-${form.id}-popup">
|
||||
<a class="action-button" href="${h.url_for( action='edit', form_id=form.id, show_form=True )}">Edit</a>
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
<form name="library" action="${h.url_for( controller='forms', action='manage' )}" method="post" >
|
||||
%if form.type == trans.app.model.FormDefinition.types.SAMPLE:
|
||||
@@ -77,58 +87,27 @@
|
||||
%endfor
|
||||
%endif
|
||||
%else:
|
||||
<table class = "grid">
|
||||
<tbody>
|
||||
%for index, field in enumerate(form.fields):
|
||||
<tr>
|
||||
<td>
|
||||
<div class="form-row">
|
||||
<label>${1+index}. Label</label>
|
||||
<a>${field['label']}</a>
|
||||
%if field['type'] == 'SelectField':
|
||||
<a id="${field['label']}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
%for option in field['selectlist']:
|
||||
<div popupmenu="${field['label']}-type-popup">
|
||||
<a class="action-button" href="" >${option}</a>
|
||||
</div>
|
||||
%endfor
|
||||
%endif
|
||||
</div>
|
||||
</td>
|
||||
<td>
|
||||
<div class="form-row">
|
||||
<label>Help text </label>
|
||||
%if not field['helptext']:
|
||||
<a><i>No helptext</i></a>
|
||||
%else:
|
||||
<a>${field['helptext']}</a>
|
||||
%endif
|
||||
</div>
|
||||
</td>
|
||||
<td>
|
||||
<div class="form-row">
|
||||
<label>Type:</label>
|
||||
<a>${field['type']}</a>
|
||||
%if field['type'] == 'SelectField':
|
||||
<a id="fieldtype-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
%for option in field['selectlist']:
|
||||
<div popupmenu="type-popup">
|
||||
<a class="action-button" href="" >${option}</a>
|
||||
</div>
|
||||
%endfor
|
||||
%endif
|
||||
</div>
|
||||
</td>
|
||||
<td>
|
||||
<div class="form-row">
|
||||
<label>Required?</label>
|
||||
<a>${field['required']}</a>
|
||||
</div>
|
||||
</td>
|
||||
</tr>
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
%for index, field in enumerate(form.fields):
|
||||
<div class="form-row">
|
||||
<label>${field['label']}</label>
|
||||
%if field['helptext']:
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${field['helptext']}</i>
|
||||
</div>
|
||||
%endif
|
||||
<div>${field['required']}</div>
|
||||
<i>Type: </i> ${field['type']}
|
||||
%if field['type'] == 'SelectField':
|
||||
<div>
|
||||
<div><i>Options:</i></div>
|
||||
%for option in field['selectlist']:
|
||||
<div>${option}</div>
|
||||
%endfor
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
%endfor
|
||||
%endif
|
||||
</form>
|
||||
</div>
|
||||
|
||||
@@ -58,6 +58,8 @@
|
||||
</select>
|
||||
%elif field['type'] == 'CheckboxField':
|
||||
<input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
|
||||
%elif field['type'] == 'NumberField':
|
||||
<input type=int name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
|
||||
%endif
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${'('+field['required']+')' }</i>
|
||||
@@ -91,35 +93,41 @@
|
||||
</%def>
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="form-row">
|
||||
<a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id )}">${details_state}</a>
|
||||
</div>
|
||||
%if details_state == "Hide request details":
|
||||
%for index, rd in enumerate(request_details):
|
||||
<div class="form-row">
|
||||
<label>${rd['label']}</label>
|
||||
%if not rd['value']:
|
||||
<i>None</i>
|
||||
%else:
|
||||
%if rd['label'] == 'Data library':
|
||||
<a href="${h.url_for( controller='library_admin', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
|
||||
%else:
|
||||
${rd['value']}
|
||||
<div class="form-row">
|
||||
%if details == "show":
|
||||
<a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id, details="hide" )}">Hide request details</a>
|
||||
</div>
|
||||
%for index, rd in enumerate(request_details):
|
||||
<div class="form-row">
|
||||
<label>${rd['label']}</label>
|
||||
%if not rd['value']:
|
||||
<i>None</i>
|
||||
%else:
|
||||
%if rd['label'] == 'Data library':
|
||||
%if rd['value']:
|
||||
<a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
|
||||
%else:
|
||||
<i>None</i>
|
||||
%endif
|
||||
%else:
|
||||
${rd['value']}
|
||||
%endif
|
||||
%endif
|
||||
%endif
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='edit', show=True, request_id=request.id)}">
|
||||
<span>Edit request details</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
%else:
|
||||
<a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id, details="show" )}">Show request details</a>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<%def name="render_grid( grid_index, grid_name, fields_dict )">
|
||||
@@ -151,13 +159,13 @@
|
||||
request.refresh()
|
||||
%>
|
||||
%for sample_index, sample in enumerate(current_samples):
|
||||
%if edit_mode:
|
||||
%if edit_mode == 'True':
|
||||
<tr>
|
||||
<td>${sample_index+1}</td>
|
||||
${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)}
|
||||
<td>
|
||||
%if request.unsubmitted() and grid_index == 0:
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
|
||||
<img src="${h.url_for('/static/images/delete_icon.png')}" />
|
||||
<span></span></a>
|
||||
%endif
|
||||
@@ -173,7 +181,7 @@
|
||||
%endif
|
||||
<td>
|
||||
%if request.unsubmitted() and grid_index == 0:
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
|
||||
<img src="${h.url_for('/static/images/delete_icon.png')}" />
|
||||
<span></span></a>
|
||||
%endif
|
||||
@@ -201,7 +209,7 @@
|
||||
<label>There are no samples.</label>
|
||||
%endif
|
||||
</div>
|
||||
%if not edit_mode:
|
||||
%if edit_mode == 'False':
|
||||
<table class="grid">
|
||||
<tbody>
|
||||
<tr>
|
||||
@@ -238,7 +246,7 @@
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
%if edit_mode:
|
||||
%if edit_mode == 'True':
|
||||
<input type="submit" name="save_samples_button" value="Save"/>
|
||||
<input type="submit" name="cancel_changes_button" value="Cancel"/>
|
||||
%elif request.unsubmitted():
|
||||
|
||||
@@ -92,41 +92,43 @@
|
||||
</%def>
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="form-row">
|
||||
<a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id )}">${details_state}</a>
|
||||
</div>
|
||||
%if details_state == "Hide request details":
|
||||
%for index, rd in enumerate(request_details):
|
||||
<div class="form-row">
|
||||
<label>${rd['label']}</label>
|
||||
%if not rd['value']:
|
||||
<i>None</i>
|
||||
%else:
|
||||
%if rd['label'] == 'Data library':
|
||||
%if rd['value']:
|
||||
<a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
|
||||
<div class="form-row">
|
||||
%if details == "show":
|
||||
<a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id, details="hide" )}">Hide request details</a>
|
||||
</div>
|
||||
%for index, rd in enumerate(request_details):
|
||||
<div class="form-row">
|
||||
<label>${rd['label']}</label>
|
||||
%if not rd['value']:
|
||||
<i>None</i>
|
||||
%else:
|
||||
%if rd['label'] == 'Data library':
|
||||
%if rd['value']:
|
||||
<a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a>
|
||||
%else:
|
||||
<i>None</i>
|
||||
%endif
|
||||
%else:
|
||||
<i>None</i>
|
||||
${rd['value']}
|
||||
%endif
|
||||
%else:
|
||||
${rd['value']}
|
||||
%endif
|
||||
%endif
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
%endfor
|
||||
%if request.unsubmitted():
|
||||
<div class="form-row">
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='edit', show=True, request_id=request.id)}">
|
||||
<span>Edit request details</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
%endfor
|
||||
%if request.unsubmitted():
|
||||
<div class="form-row">
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='edit', show=True, request_id=request.id)}">
|
||||
<span>Edit request details</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
%else:
|
||||
<a href="${h.url_for( controller='requests', action='toggle_request_details', request_id=request.id, details="show" )}">Show request details</a>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<%def name="render_grid( grid_index, grid_name, fields_dict )">
|
||||
@@ -158,7 +160,7 @@
|
||||
request.refresh()
|
||||
%>
|
||||
%for sample_index, sample in enumerate(current_samples):
|
||||
%if edit_mode:
|
||||
%if edit_mode == 'True':
|
||||
<tr>
|
||||
<td>${sample_index+1}</td>
|
||||
${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)}
|
||||
@@ -194,7 +196,7 @@
|
||||
|
||||
<div class="toolForm">
|
||||
##<div class="toolFormTitle">Samples (${len(request.samples)})</div>
|
||||
<form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request' )}" enctype="multipart/form-data" method="post" >
|
||||
<form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
|
||||
<div class="form-row">
|
||||
%if current_samples:
|
||||
%if not request.type.sample_form.layout:
|
||||
@@ -211,7 +213,7 @@
|
||||
%endif
|
||||
|
||||
</div>
|
||||
%if request.unsubmitted() and not edit_mode:
|
||||
%if request.unsubmitted() and edit_mode == 'False':
|
||||
<table class="grid">
|
||||
<tbody>
|
||||
<tr>
|
||||
@@ -251,7 +253,7 @@
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save_samples_button" value="Save"/>
|
||||
%if edit_mode:
|
||||
%if edit_mode == 'True':
|
||||
<input type="submit" name="cancel_changes_button" value="Cancel"/>
|
||||
%endif
|
||||
</div>
|
||||
|
||||
@@ -46,7 +46,7 @@
|
||||
<td>
|
||||
<div class="form-row">
|
||||
<label>${address.desc}</label>
|
||||
${address.display()}
|
||||
${address.get_html()}
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<ul class="manage-table-actions">
|
||||
|
||||
+28
-12
@@ -1059,8 +1059,15 @@ class TwillTestCase( unittest.TestCase ):
|
||||
tc.fv( "1", field_name, field_contents )
|
||||
tc.fv( "1", field_help_name, field_help_contents )
|
||||
tc.submit( "save_changes_button" )
|
||||
if num_fields:
|
||||
check_str = "The form '%s' has been updated with the changes." % name
|
||||
self.check_page_for_string( check_str )
|
||||
self.check_page_for_string( check_str )
|
||||
else:
|
||||
self.home()
|
||||
self.visit_url( "%s/forms/manage" % self.url )
|
||||
self.check_page_for_string( name )
|
||||
self.check_page_for_string( desc )
|
||||
self.check_page_for_string( formtype )
|
||||
self.home()
|
||||
def edit_form( self, form_id, form_name, new_form_name="Form One's Name (Renamed)", new_form_desc="This is Form One's description (Re-described)"):
|
||||
"""
|
||||
@@ -1074,7 +1081,7 @@ class TwillTestCase( unittest.TestCase ):
|
||||
tc.submit( "save_changes_button" )
|
||||
self.check_page_for_string( "The form '%s' has been updated with the changes." % new_form_name )
|
||||
self.home()
|
||||
def form_add_field( self, form_id, form_name, field_index, fields):
|
||||
def form_add_field( self, form_id, form_name, form_desc, form_type, field_index, fields):
|
||||
"""
|
||||
Add a new fields to the form definition
|
||||
"""
|
||||
@@ -1088,13 +1095,18 @@ class TwillTestCase( unittest.TestCase ):
|
||||
tc.fv( "1", "field_helptext_%i" % index, field['desc'] )
|
||||
tc.fv( "1", "field_type_%i" % index, field['type'] )
|
||||
tc.fv( "1", "field_required_%i" % index, field['required'] )
|
||||
# if field['type'] == 'SelectField':
|
||||
# for option_index, option in enumerate(field['selectlist']):
|
||||
# self.visit_url( "%s/forms/edit?select_box_options=add&form_id=%i&field_index=%i" % \
|
||||
# (self.url, form_id, index))
|
||||
# #data = self.last_page()
|
||||
# #file( "rc.html", 'wb' ).write(data)
|
||||
# tc.fv( "1", "field_%i_option_%i" % (index, option_index), option )
|
||||
if field['type'] == 'SelectField':
|
||||
options = ''
|
||||
for option_index, option in enumerate(field['selectlist']):
|
||||
url_str = "%s/forms/edit?description=%s&form_id=%i&form_type_selectbox=%s&addoption_%i=Add&name=%s&field_name_%i=%s&field_helptext_%i=%s&field_type_%i=%s" % \
|
||||
(self.url, form_desc.replace(" ", "+"), form_id, form_type.replace(" ", "+"),
|
||||
index, form_name.replace(" ", "+"), index, field['name'].replace(" ", "+"),
|
||||
index, field['desc'].replace(" ", "+"), index, field['type'])
|
||||
self.visit_url( url_str + options )
|
||||
data = self.last_page()
|
||||
file( "rc.html", 'wb' ).write(data)
|
||||
tc.fv( "1", "field_%i_option_%i" % (index, option_index), option )
|
||||
options = options + "&field_%i_option_%i=%s" % (index, option_index, option)
|
||||
tc.submit( "save_changes_button" )
|
||||
check_str = "The form '%s' has been updated with the changes." % form_name
|
||||
self.check_page_for_string( check_str )
|
||||
@@ -1130,18 +1142,22 @@ class TwillTestCase( unittest.TestCase ):
|
||||
self.check_page_for_string( "Request type <b>%s</b> has been created" % name )
|
||||
def create_request( self, request_type_id, name, desc, library_id, folder_id, fields ):
|
||||
self.home()
|
||||
self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % (self.url, request_type_id) )
|
||||
self.visit_url( "%s/requests/new?create=True&select_request_type=%i&library_id=%i" % ( self.url,
|
||||
request_type_id,
|
||||
library_id ) )
|
||||
self.check_page_for_string( 'Add a new request' )
|
||||
tc.fv( "1", "name", name )
|
||||
tc.fv( "1", "desc", desc )
|
||||
tc.fv( "1", "library_id", str(library_id) )
|
||||
#tc.fv( "1", "folder_id", str(folder_id) )
|
||||
tc.fv( "1", "folder_id", str(folder_id) )
|
||||
for index, field_value in enumerate(fields):
|
||||
tc.fv( "1", "field_%i" % index, field_value )
|
||||
tc.submit( "create_request_button" )
|
||||
def create_request_admin( self, request_type_id, user_id, name, desc, library_id, fields ):
|
||||
self.home()
|
||||
self.visit_url( "%s/requests_admin/new?create=True&select_request_type=%i" % (self.url, request_type_id) )
|
||||
self.visit_url( "%s/requests_admin/new?create=True&select_request_type=%i&library_id=%i" % ( self.url,
|
||||
request_type_id,
|
||||
library_id ) )
|
||||
self.check_page_for_string( 'Add a new request' )
|
||||
tc.fv( "1", "select_user", str(user_id) )
|
||||
tc.fv( "1", "name", name )
|
||||
|
||||
@@ -42,12 +42,7 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
name = form_one_name
|
||||
desc = "This is Form One's description"
|
||||
formtype = galaxy.model.FormDefinition.types.REQUEST
|
||||
self.create_form( name=name, desc=desc, formtype=formtype )
|
||||
self.home()
|
||||
self.visit_page( 'forms/manage' )
|
||||
self.check_page_for_string( name )
|
||||
self.check_page_for_string( desc )
|
||||
self.check_page_for_string( formtype )
|
||||
self.create_form( name=name, desc=desc, formtype=formtype, num_fields=0 )
|
||||
# Get the form_definition object for later tests
|
||||
form_one = galaxy.model.FormDefinition.filter( and_( galaxy.model.FormDefinition.table.c.name==name,
|
||||
galaxy.model.FormDefinition.table.c.desc==desc,
|
||||
@@ -66,24 +61,21 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
"""Testing adding fields to a form definition"""
|
||||
fields = [dict(name='Test field name one',
|
||||
desc='Test field description one',
|
||||
type='TextField',
|
||||
required='required'),
|
||||
type='SelectField',
|
||||
required='optional',
|
||||
selectlist=['option1', 'option2']),
|
||||
dict(name='Test field name two',
|
||||
desc='Test field description two',
|
||||
type='AddressField',
|
||||
required='optional')]
|
||||
required='optional'),
|
||||
dict(name='Test field name three',
|
||||
desc='Test field description three',
|
||||
type='TextField',
|
||||
required='required')]
|
||||
form_one = get_latest_form(form_one_name)
|
||||
self.form_add_field(form_one.id, form_one.name, field_index=len(form_one.fields), fields=fields)
|
||||
self.form_add_field(form_one.id, form_one.name, form_one.desc, form_one.type, field_index=len(form_one.fields), fields=fields)
|
||||
form_one_latest = get_latest_form(form_one_name)
|
||||
assert len(form_one_latest.fields) == len(form_one.fields)+len(fields)
|
||||
#This following test has been commented out as it is causing:
|
||||
#TwillException: multiple matches to "remove_button"
|
||||
# def test_010_remove_form_fields( self ):
|
||||
# """Testing removing fields from a form definition"""
|
||||
# form_one = get_latest_form(form_one_name)
|
||||
# self.form_remove_field( form_one.id, form_one.name, 'Test field name one' )
|
||||
# form_one_latest = get_latest_form(form_one_name)
|
||||
# assert len(form_one_latest.fields) == len(form_one.fields)-1
|
||||
def test_015_create_sample_form( self ):
|
||||
"""Testing creating another form (for samples)"""
|
||||
global form_two_name
|
||||
@@ -186,10 +178,10 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email='test1@bx.psu.edu' )
|
||||
# set field values
|
||||
fields = ['field one value', 'field two value', str(user_address.id)]
|
||||
fields = ['option1', str(user_address.id), 'field three value']
|
||||
# create the request
|
||||
request_name, request_desc = 'Request One', 'Request One Description'
|
||||
self.create_request(request_type.id, request_name, request_desc, library_one.id, folder_one.id, fields)
|
||||
self.create_request(request_type.id, request_name, request_desc, library_one.id, 'none', fields)
|
||||
self.check_page_for_string( request_name )
|
||||
self.check_page_for_string( request_desc )
|
||||
global request_one
|
||||
@@ -208,8 +200,9 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
for field_value in fields:
|
||||
self.check_page_for_string( field_value )
|
||||
# edit this request
|
||||
fields = ['field one value (edited)', 'field two value (edited)', str(user_address.id)]
|
||||
self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields)
|
||||
fields = ['option2', str(user_address.id), 'field three value (edited)']
|
||||
self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)',
|
||||
request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields)
|
||||
request_one.refresh()
|
||||
self.check_page_for_string( request_name+' (Renamed)' )
|
||||
self.check_page_for_string( request_desc+' (Re-described)' )
|
||||
@@ -261,8 +254,8 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
self.login( email='test@bx.psu.edu' )
|
||||
request_name = "RequestTwo"
|
||||
# simulate request creation
|
||||
url_str = '%s/requests_admin/new?create=True&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&library_id=%i&folder_id=%i&refresh=True&field_1=%s&field_2=%i' \
|
||||
% ( self.url, request_type.id, regular_user.id, request_name, library_one.id, library_one.root_folder.id, "field_1_value", user_address.id )
|
||||
url_str = '%s/requests_admin/new?create=True&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&library_id=%i&folder_id=%i&refresh=True&field_2=%s&field_0=%s&field_1=%i' \
|
||||
% ( self.url, request_type.id, regular_user.id, request_name, library_one.id, library_one.root_folder.id, "field_2_value", 'option1', user_address.id )
|
||||
self.home()
|
||||
self.visit_url( url_str )
|
||||
self.check_page_for_string( "The new request named %s has been created" % request_name )
|
||||
@@ -299,10 +292,3 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
self.visit_url( '%s/requests_admin/list?show_filter=All' % self.url )
|
||||
self.check_page_for_string( request_one.name )
|
||||
self.check_page_for_string( request_two.name )
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user