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galaxy/test/functional/test_library_templates.py
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from base.twilltestcase import TwillTestCase
from base.test_db_util import (
get_user,
get_private_role,
get_form,
get_library,
get_folder,
get_user_address,
get_latest_ldda_by_name,
get_latest_hda,
mark_obj_deleted,
refresh
)
import galaxy.model
AddressField_form = None
CheckboxField_form = None
SelectField_form = None
TextArea_form = None
TextField_form = None
WorkflowField_form = None
address_field_name = checkbox_field_name = select_field_name = None
workflow_field_name = textfield_name = textarea_name = None
user_address1 = user_address2 = None
ldda1 = library1 = library2 = library3 = library4 = library5 = library6 = None
folder1 = folder2 = folder3 = folder4 = folder5 = folder6 = None
admin_user = None
regular_user1 = regular_user2 = regular_user3 = None
class TestLibraryFeatures( TwillTestCase ):
def test_000_initiate_users( self ):
"""Ensuring all required user accounts exist"""
self.logout()
self.login( email='test1@bx.psu.edu', username='regular-user1' )
global regular_user1
regular_user1 = get_user( 'test1@bx.psu.edu' )
assert regular_user1 is not None, 'Problem retrieving user with email "test1@bx.psu.edu" from the database'
global regular_user1_private_role
regular_user1_private_role = get_private_role( regular_user1 )
self.logout()
self.login( email='test2@bx.psu.edu', username='regular-user2' )
global regular_user2
regular_user2 = get_user( 'test2@bx.psu.edu' )
assert regular_user2 is not None, 'Problem retrieving user with email "test2@bx.psu.edu" from the database'
global regular_user2_private_role
regular_user2_private_role = get_private_role( regular_user2 )
self.logout()
self.login( email='test3@bx.psu.edu', username='regular-user3' )
global regular_user3
regular_user3 = get_user( 'test3@bx.psu.edu' )
assert regular_user3 is not None, 'Problem retrieving user with email "test3@bx.psu.edu" from the database'
global regular_user3_private_role
regular_user3_private_role = get_private_role( regular_user3 )
self.logout()
self.login( email='test@bx.psu.edu', username='admin-user' )
global admin_user
admin_user = get_user( 'test@bx.psu.edu' )
assert admin_user is not None, 'Problem retrieving user with email "test@bx.psu.edu" from the database'
global admin_user_private_role
admin_user_private_role = get_private_role( admin_user )
def test_005_create_library_templates( self ):
"""Testing creating several LibraryInformationTemplate form definitions"""
# Logged in as admin_user
for type in [ 'AddressField', 'CheckboxField', 'SelectField', 'TextArea', 'TextField', 'WorkflowField' ]:
field_name = type.lower()
form_desc = '%s description' % type
num_options = 0
if type == 'SelectField':
# Pass number of options we want in our SelectField
num_options = 2
# Create form for library template
strings_displayed_after_submit = [ "The form '%s' has been updated with the changes." % type ]
self.create_form( name=type,
description=form_desc,
form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE,
field_type=type,
num_options=num_options,
field_name=field_name,
strings_displayed_after_submit=strings_displayed_after_submit )
# Get all of the new form definitions for later use
global AddressField_form
AddressField_form = get_form( 'AddressField' )
# NOTE: each of these names need to be the same as field_name defined above
# for each type.
global address_field_name
address_field_name = 'addressfield'
global CheckboxField_form
CheckboxField_form = get_form( 'CheckboxField' )
global checkbox_field_name
checkbox_field_name = 'checkboxfield'
global SelectField_form
SelectField_form = get_form( 'SelectField' )
global select_field_name
select_field_name = 'selectfield'
global TextArea_form
TextArea_form = get_form( 'TextArea' )
global textarea_name
textarea_name = 'textarea'
global TextField_form
TextField_form = get_form( 'TextField' )
global textfield_name
textfield_name = 'textfield'
global WorkflowField_form
WorkflowField_form = get_form( 'WorkflowField' )
global workflow_field_name
workflow_field_name = 'workflowfield'
def test_010_create_libraries( self ):
"""Testing creating a new library for each template"""
# Logged in as admin_user
# library1 -> AddressField
# library2 -> CheckboxField
# library3 -> SelectField
# library4 -> TextArea
# library5 -> TextField
# library6 -> WorkflowField
for index, form in enumerate( [ AddressField_form, CheckboxField_form, SelectField_form, TextArea_form, TextField_form, WorkflowField_form ] ):
name = 'library%s' % str( index + 1 )
description = '%s description' % name
synopsis = '%s synopsis' % name
self.create_library( name=name, description=description, synopsis=synopsis )
# Get the libraries for later use
global library1
library1 = get_library( 'library1', 'library1 description', 'library1 synopsis' )
global library2
library2 = get_library( 'library2', 'library2 description', 'library2 synopsis' )
global library3
library3 = get_library( 'library3', 'library3 description', 'library3 synopsis' )
global library4
library4 = get_library( 'library4', 'library4 description', 'library4 synopsis' )
global library5
library5 = get_library( 'library5', 'library5 description', 'library5 synopsis' )
global library6
library6 = get_library( 'library6', 'library6 description', 'library6 synopsis' )
def test_015_add_template_to_library1( self ):
"""Testing add an inheritable template containing an AddressField to library1"""
# Logged in as admin_user
# Add a template containing an AddressField to library1
self.add_template( cntrller='library_admin',
item_type='library',
form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE,
form_id=self.security.encode_id( AddressField_form.id ),
form_name=AddressField_form.name,
library_id=self.security.encode_id( library1.id ) )
def test_020_add_folder_to_library1( self ):
"""Testing adding a folder to library1"""
# Logged in as admin_user
# Add a folder to library1
folder = library1.root_folder
name = "folder"
description = "folder description"
self.add_folder( 'library_admin',
self.security.encode_id( library1.id ),
self.security.encode_id( folder.id ),
name=name,
description=description )
global folder1
folder1 = get_folder( folder.id, name, description )
def test_025_check_library1( self ):
"""Checking library1 and its root folder"""
# Logged in as admin_user
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library1.id ),
strings_displayed=[ folder1.name, folder1.description ] )
# Make sure the template and contents were inherited to folder1
self.folder_info( cntrller='library_admin',
folder_id=self.security.encode_id( folder1.id ),
library_id=self.security.encode_id( library1.id ),
template_refresh_field_name=address_field_name,
strings_displayed=[ AddressField_form.name,
'This is an inherited template and is not required to be used with this folder' ] )
def test_030_add_dataset_to_folder1( self ):
"""Testing adding a ldda1 to folder1, and adding a new UserAddress on the upload form."""
# Logged in as admin_user
# The AddressField template should be inherited to the library dataset upload form. Passing
# the value 'new' should submit the form via refresh_on_change and allow new UserAddress information
# to be posted as part of the upload.
filename = '1.bed'
ldda_message = '1.bed message'
short_desc = 'Office'
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library1.id ),
folder_id=self.security.encode_id( folder1.id ),
filename=filename,
file_type='bed',
dbkey='hg18',
template_refresh_field_name=address_field_name,
ldda_message=ldda_message,
template_refresh_field_contents='new',
template_fields=[ ( '%s_short_desc' % address_field_name, short_desc ),
( '%s_name' % address_field_name, 'Dick' ),
( '%s_institution' % address_field_name, 'PSU' ),
( '%s_address' % address_field_name, '32 O Street' ),
( '%s_city' % address_field_name, 'Anywhere' ),
( '%s_state' % address_field_name, 'AK' ),
( '%s_postal_code' % address_field_name, '0000000' ),
( '%s_country' % address_field_name, 'USA' ) ],
strings_displayed=[ 'Upload files' ] )
global user_address1
user_address1 = get_user_address( admin_user, short_desc )
assert user_address1 is not None, 'Problem retrieving user_address1 from the database'
global ldda1
ldda1 = get_latest_ldda_by_name( filename )
assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda1.name, ldda1.message, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library1.id ),
self.security.encode_id( folder1.id ),
self.security.encode_id( ldda1.id ),
ldda1.name,
strings_displayed=[ 'Dick' ] )
def test_035_edit_contents_of_ldda1_tempplate( self ):
"""Testing editing the contents of ldda1 AddressField template by adding a new user_address"""
short_desc = 'Home'
# Now add a new user_address to ldda1
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library1.id ),
self.security.encode_id( folder1.id ),
self.security.encode_id( ldda1.id ),
ldda1.name,
template_refresh_field_name=address_field_name,
template_refresh_field_contents='new',
template_fields=[ ( '%s_short_desc' % address_field_name, short_desc ),
( '%s_name' % address_field_name, 'Richard' ),
( '%s_institution' % address_field_name, 'PSU' ),
( '%s_address' % address_field_name, '32 O Street' ),
( '%s_city' % address_field_name, 'Anywhere' ),
( '%s_state' % address_field_name, 'AK' ),
( '%s_postal_code' % address_field_name, '0000000' ),
( '%s_country' % address_field_name, 'USA' ) ],
strings_displayed=[ short_desc ] )
global user_address2
user_address2 = get_user_address( admin_user, short_desc )
assert user_address2 is not None, 'Problem retrieving user_address2 from the database'
def test_040_edit_contents_of_folder1_template( self ):
"""Testing editing the contents of folder1 AddressField template"""
# Make sure the template and contents were inherited to folder1
self.folder_info( cntrller='library_admin',
folder_id=self.security.encode_id( folder1.id ),
library_id=self.security.encode_id( library1.id ),
template_refresh_field_name=address_field_name,
template_refresh_field_contents=str( user_address2.id ),
strings_displayed=[ AddressField_form.name,
'This is an inherited template and is not required to be used with this folder' ],
strings_displayed_after_submit=[ 'Richard' ] )
def test_045_add_dataset_to_folder1( self ):
"""Testing adding another ldda to folder1"""
# The upload form should now inherit user_address2 on the upload form
filename = '2.bed'
ldda_message = '2.bed message'
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library1.id ),
folder_id=self.security.encode_id( folder1.id ),
filename=filename,
file_type='bed',
dbkey='hg18',
template_refresh_field_name=address_field_name,
ldda_message=ldda_message,
strings_displayed=[ 'Upload files' ] )
# Make sure user_address2 is associated with ldda.
self.ldda_edit_info( cntrller='library_admin',
library_id=self.security.encode_id( library1.id ),
folder_id=self.security.encode_id( folder1.id ),
ldda_id=self.security.encode_id( ldda1.id ),
ldda_name=ldda1.name,
template_refresh_field_name=address_field_name,
strings_displayed=[ user_address2.desc ] )
def test_050_add_template_to_library2( self ):
""" Testing add an inheritable template containing an CheckboxField to library2"""
# Add a template containing an CheckboxField to library1
self.add_template( cntrller='library_admin',
item_type='library',
form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE,
form_id=self.security.encode_id( CheckboxField_form.id ),
form_name=CheckboxField_form.name,
library_id=self.security.encode_id( library2.id ) )
# Check the CheckboxField to make sure the template contents are inherited
self.library_info( 'library_admin',
self.security.encode_id( library2.id ),
template_fields=[ ( checkbox_field_name, '1' ) ] )
def test_055_add_folder2_to_library2( self ):
"""Testing adding a folder to library2"""
# Logged in as admin_user
# Add a folder to library2
folder = library2.root_folder
name = "folder"
description = "folder description"
self.add_folder( 'library_admin',
self.security.encode_id( library2.id ),
self.security.encode_id( folder.id ),
name=name,
description=description )
global folder2
folder2 = get_folder( folder.id, name, description )
def test_060_check_library2( self ):
"""Checking library2 and its root folder"""
# Logged in as admin_user
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library2.id ),
strings_displayed=[ folder2.name, folder2.description ] )
def test_065_save_folder2_inherited_template( self ):
"""Saving the inherited template for folder2"""
# Logged in as admin_user
# Save the inherited template
self.folder_info( cntrller='library_admin',
folder_id=self.security.encode_id( folder2.id ),
library_id=self.security.encode_id( library2.id ),
template_fields=[ ( checkbox_field_name, '1' ) ],
strings_displayed=[ CheckboxField_form.name,
'This is an inherited template and is not required to be used with this folder' ] )
def test_070_add_ldda_to_folder2( self ):
"""
Testing adding a new library dataset to library2's folder, making sure the CheckboxField is
checked on the upload form.
"""
# Logged in as admin_user
filename = '1.bed'
ldda_message = '1.bed message'
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library2.id ),
folder_id=self.security.encode_id( folder2.id ),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=[ 'CheckboxField', 'checked' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library2.id ),
strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library2.id ),
self.security.encode_id( folder2.id ),
self.security.encode_id( ldda.id ),
ldda.name,
strings_displayed=[ 'CheckboxField', 'checked' ] )
def test_080_add_template_to_library3( self ):
""" Testing add an inheritable template containing an SelectField to library3"""
# Logged in as admin_user
self.add_template( cntrller='library_admin',
item_type='library',
form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE,
form_id=self.security.encode_id( SelectField_form.id ),
form_name=SelectField_form.name,
library_id=self.security.encode_id( library3.id ) )
# Select the 2nd option in the SelectField to make sure the template contents are inherited
# SelectField option names are zero-based
self.library_info( 'library_admin',
self.security.encode_id( library3.id ),
template_fields=[ ( select_field_name, 'Option1' ) ] )
def test_085_add_folder3_to_library3( self ):
"""Testing adding a folder to library3"""
# Logged in as admin_user
# Add a folder to library3
folder = library3.root_folder
name = "folder"
description = "folder description"
self.add_folder( 'library_admin',
self.security.encode_id( library3.id ),
self.security.encode_id( folder.id ),
name=name,
description=description )
global folder3
folder3 = get_folder( folder.id, name, description )
def test_090_check_library3( self ):
"""Checking library3 and its root folder"""
# Logged in as admin_user
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library3.id ),
strings_displayed=[ folder3.name, folder3.description ] )
def test_095_save_folder3_inherited_template( self ):
"""Saving the inherited template for folder3"""
# Logged in as admin_user
# Save the inherited template
self.folder_info( cntrller='library_admin',
folder_id=self.security.encode_id( folder3.id ),
library_id=self.security.encode_id( library3.id ),
template_fields=[ ( select_field_name, 'Option1' ) ],
strings_displayed=[ SelectField_form.name,
'This is an inherited template and is not required to be used with this folder',
'Option1' ] )
def test_100_add_ldda_to_folder3( self ):
"""
Testing adding a new library dataset to library3's folder, making sure the SelectField setting is correct on the upload form.
"""
filename = '3.bed'
ldda_message = '3.bed message'
# Logged in as admin_user
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library3.id ),
folder_id=self.security.encode_id( folder3.id ),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=[ 'SelectField', 'selected>Option1' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library3.id ),
strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library3.id ),
self.security.encode_id( folder3.id ),
self.security.encode_id( ldda.id ),
ldda.name,
strings_displayed=[ 'SelectField', 'Option1' ] )
# Import a dataset from the current history
filename = '8.bed'
self.new_history( name='import+with+SelectField' )
self.upload_file( filename )
hda = get_latest_hda()
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library3.id ),
folder_id=self.security.encode_id( folder3.id ),
upload_option='import_from_history',
hda_ids=self.security.encode_id( hda.id ),
strings_displayed=[ '<select name="%s" last_selected_value="Option1">' % select_field_name ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library3.id ),
strings_displayed=[ ldda.name, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library3.id ),
self.security.encode_id( folder3.id ),
self.security.encode_id( ldda.id ),
ldda.name,
strings_displayed=[ 'SelectField', 'Option1' ] )
def test_105_add_template_to_library4( self ):
""" Testing add an inheritable template containing an TextArea to library4"""
# Logged in as admin_user
# Add an inheritable template to library4
self.add_template( cntrller='library_admin',
item_type='library',
form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE,
form_id=self.security.encode_id( TextArea_form.id ),
form_name=TextArea_form.name,
library_id=self.security.encode_id( library4.id ) )
# Select the 2nd option in the SelectField to make sure the template contents are inherited
self.library_info( 'library_admin',
self.security.encode_id( library4.id ),
template_fields=[ ( textarea_name, 'This text should be inherited' ) ] )
def test_110_add_folder4_to_library4( self ):
"""Testing adding a folder to library4"""
# Logged in as admin_user
# Add a folder to library4
folder = library4.root_folder
name = "folder"
description = "folder description"
self.add_folder( 'library_admin',
self.security.encode_id( library4.id ),
self.security.encode_id( folder.id ),
name=name,
description=description )
global folder4
folder4 = get_folder( folder.id, name, description )
def test_115_save_folder4_inherited_template( self ):
"""Saving the inherited template for folder4"""
# Logged in as admin_user
# Save the inherited template
self.folder_info( cntrller='library_admin',
folder_id=self.security.encode_id( folder4.id ),
library_id=self.security.encode_id( library4.id ),
template_fields=[ ( textarea_name, 'This text should be inherited' ) ],
strings_displayed=[ TextArea_form.name,
'This is an inherited template and is not required to be used with this folder',
'This text should be inherited' ] )
def test_120_add_ldda_to_folder4( self ):
"""
Testing adding a new library dataset to library4's folder, making sure the TextArea setting is correct on the upload form.
"""
filename = '4.bed'
ldda_message = '4.bed message'
# Logged in as admin_user
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library4.id ),
folder_id=self.security.encode_id( folder4.id ),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=[ 'TextArea', 'This text should be inherited' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library4.id ),
strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library4.id ),
self.security.encode_id( folder4.id ),
self.security.encode_id( ldda.id ),
ldda.name,
strings_displayed=[ 'TextArea', 'This text should be inherited' ] )
def test_125_add_template_to_library5( self ):
""" Testing add an inheritable template containing an TextField to library5"""
# Add an inheritable template to library5
self.add_template( cntrller='library_admin',
item_type='library',
form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE,
form_id=self.security.encode_id( TextField_form.id ),
form_name=TextField_form.name,
library_id=self.security.encode_id( library5.id ) )
# Select the 2nd option in the SelectField to make sure the template contents are inherited
self.library_info( 'library_admin',
self.security.encode_id( library5.id ),
template_fields=[ ( textfield_name, 'This text should be inherited' ) ] )
def test_130_add_folder5_to_library5( self ):
"""Testing adding a folder to library5"""
# Logged in as admin_user
# Add a folder to library5
folder = library5.root_folder
name = "folder"
description = "folder description"
self.add_folder( 'library_admin',
self.security.encode_id( library5.id ),
self.security.encode_id( folder.id ),
name=name,
description=description )
global folder5
folder5 = get_folder( folder.id, name, description )
def test_135_save_folder5_inherited_template( self ):
"""Saving the inherited template for folder5"""
# Logged in as admin_user
# Save the inherited template
self.folder_info( cntrller='library_admin',
folder_id=self.security.encode_id( folder5.id ),
library_id=self.security.encode_id( library5.id ),
template_fields=[ ( textfield_name, 'This text should be inherited' ) ],
strings_displayed=[ TextField_form.name,
'This is an inherited template and is not required to be used with this folder',
'This text should be inherited' ] )
def test_140_add_ldda_to_folder5( self ):
"""
Testing adding a new library dataset to library5's folder, making sure the TextField setting is correct on the upload form.
"""
# Logged in as admin_user
filename = '5.bed'
ldda_message = '5.bed message'
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library5.id ),
folder_id=self.security.encode_id( folder5.id ),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=[ 'TextField', 'This text should be inherited' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library5.id ),
strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library5.id ),
self.security.encode_id( folder5.id ),
self.security.encode_id( ldda.id ),
ldda.name,
strings_displayed=[ 'TextField', 'This text should be inherited' ] )
def test_145_edit_library5_template_layout( self ):
"""Test editing the layout of library5's template"""
# Currently there is only a TextField, and we'll add a TextArea.
self.edit_template( cntrller='library_admin',
item_type='library',
form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE,
library_id=self.security.encode_id( library5.id ),
field_type='TextArea',
field_label_1=TextArea_form.name,
field_helptext_1='%s help' % TextArea_form.name,
field_default_1='%s default' % TextArea_form.name )
def test_150_add_ldda_to_library5( self ):
"""
Testing adding a new library dataset to library5's folder, making sure the TextField and new TextArea settings are correct on the upload form.
"""
filename = '6.bed'
ldda_message = '6.bed message'
# Logged in as admin_user
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library5.id ),
folder_id=self.security.encode_id( library5.root_folder.id ),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=[ 'TextField',
'This text should be inherited',
'TextArea' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library5.id ),
strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library5.id ),
self.security.encode_id( library5.root_folder.id ),
self.security.encode_id( ldda.id ),
ldda.name,
strings_displayed=[ 'TextField',
'This text should be inherited',
'TextArea' ] )
def test_155_add_template_to_library6( self ):
""" Testing add an inheritable template containing an WorkflowField to library6"""
# Add an inheritable template to library6
# We won't select an option since we have no workflow to select
self.add_template( cntrller='library_admin',
item_type='library',
form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE,
form_id=self.security.encode_id( WorkflowField_form.id ),
form_name=WorkflowField_form.name,
library_id=self.security.encode_id( library6.id ) )
def test_160_add_folder6_to_library6( self ):
"""Testing adding a folder to library6"""
# Logged in as admin_user
# Add a folder to library5
folder = library6.root_folder
name = "folder"
description = "folder description"
self.add_folder( 'library_admin',
self.security.encode_id( library6.id ),
self.security.encode_id( folder.id ),
name=name,
description=description )
global folder6
folder6 = get_folder( folder.id, name, description )
def test_165_save_folder6_inherited_template( self ):
"""Saving the inherited template for folder6"""
# Logged in as admin_user
# Save the inherited template - we won't select an option since we have no workflow to select
self.folder_info( cntrller='library_admin',
folder_id=self.security.encode_id( folder6.id ),
library_id=self.security.encode_id( library6.id ),
template_fields=[ ( workflow_field_name, 'none' ) ],
strings_displayed=[ WorkflowField_form.name,
'This is an inherited template and is not required to be used with this folder',
'none' ] )
def test_170_add_ldda_to_folder6( self ):
"""
Testing adding a new library dataset to library6's folder, making sure the WorkflowField setting is correct on the upload form.
"""
# Logged in as admin_user
filename = '7.bed'
ldda_message = '7.bed message'
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library6.id ),
folder_id=self.security.encode_id( folder6.id ),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=[ 'WorkflowField', 'none' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
self.browse_library( cntrller='library_admin',
library_id=self.security.encode_id( library6.id ),
strings_displayed=[ ldda.name, ldda.message, 'bed' ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
self.security.encode_id( library6.id ),
self.security.encode_id( folder6.id ),
self.security.encode_id( ldda.id ),
ldda.name,
strings_displayed=[ 'WorkflowField', 'none' ] )
def test_999_reset_data_for_later_test_runs( self ):
"""Reseting data to enable later test runs to pass"""
# Logged in as admin_user
##################
# Delete all form definitions
##################
for form in [ AddressField_form, CheckboxField_form, SelectField_form, TextArea_form, TextField_form, WorkflowField_form ]:
self.mark_form_deleted( self.security.encode_id( form.form_definition_current.id ) )
##################
# Mark all user_addresses deleted
##################
for user_address in [ user_address1, user_address2 ]:
mark_obj_deleted( user_address )
##################
# Purge all libraries
##################
for library in [ library1, library2, library3, library4, library5, library6 ]:
self.delete_library_item( 'library_admin',
self.security.encode_id( library.id ),
self.security.encode_id( library.id ),
library.name,
item_type='library' )
self.purge_library( self.security.encode_id( library.id ), library.name )
##################
# Make sure all users are associated only with their private roles
##################
for user in [ admin_user, regular_user1, regular_user2, regular_user3 ]:
refresh( user )
if len( user.roles) != 1:
raise AssertionError( '%d UserRoleAssociations are associated with %s ( should be 1 )' % ( len( user.roles ), user.email ) )
self.logout()
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