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_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_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_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_040_create_ldda2_with_role2_associated_with_group_and_users( self ):
"""Testing creating ldda2 with a role that is associated with a group and users"""
# Logged in as admin_user
# Add a dataset restricted by role2, which is currently associated as follows:
# groups: group1
# users: [email protected], [email protected] via group1
#
# We first need to make library1 public, but leave its contents permissions unchanged
self.make_library_item_public( self.security.encode_id( library1.id ),
self.security.encode_id( library1.id ),
item_type='library',
contents=False,
library_name=library1.name )
refresh( library1 )
filename = '2.bed'
ldda_message = 'ldda2'
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='hg17',
roles=[ str( role2.id ) ],
ldda_message=ldda_message,
strings_displayed=[ 'Upload files' ] )
global ldda2
ldda2 = get_latest_ldda_by_name( filename )
assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database'
self.browse_library( cntrller='library',
library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] )
def test_075_download_archive_of_library_files(self):
"""Testing downloading an archive of files from library1"""
# logged in as regular_user3
self.logout()
self.login(email=admin_user.email)
filename = '1.bed'
self.upload_library_dataset(
cntrller='library_admin',
library_id=self.security.encode_id(library1.id),
folder_id=self.security.encode_id(library1.root_folder.id),
filename=filename,
file_type='bed',
dbkey='hg18',
strings_displayed=['Upload files'])
global ldda1
ldda1 = get_latest_ldda_by_name(filename)
assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database'
for format in ('tbz', 'tgz', 'zip'):
archive = self.download_archive_of_library_files(
cntrller='library',
library_id=self.security.encode_id(library1.id),
ldda_ids=[
self.security.encode_id(ldda1.id),
self.security.encode_id(ldda2.id)
],
format=format)
self.check_archive_contents(archive, (ldda1, ldda2))
os.remove(archive)
def test_025_create_ldda1_with_private_role_restriction( self ):
"""Testing create ldda1 with a private role restriction"""
# Logged in as admin_user
#
# Library1 LIBRARY_ACCESS = Role1: admin_user, regular_user1, regular_user3
#
# Add a dataset restricted by the following:
# DATASET_MANAGE_PERMISSIONS = admin_user via DefaultUserPermissions
# DATASET_ACCESS = regular_user1 private role via this test method
# LIBRARY_ADD = "Role1" via inheritance from parent folder
# LIBRARY_MODIFY = "Role1" via inheritance from parent folder
# LIBRARY_MANAGE = "Role1" via inheritance from parent folder
#
# This means that only regular_user1 can see the dataset from the Data Libraries view
filename = '1.bed'
ldda_message = 'ldda1'
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',
roles=[ str( regular_user1_private_role.id ) ],
ldda_message=ldda_message,
strings_displayed=[ 'Upload files' ] )
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' ] )
def test_085_create_ldda8( self ):
"""Testing create ldda8, restricting access on upload form to admin_user's private role"""
filename = '8.bed'
ldda_message = 'ldda8'
self.upload_library_dataset( cntrller='library_admin',
library_id=self.security.encode_id( library2.id ),
folder_id=self.security.encode_id( subfolder2.id ),
filename=filename,
file_type='bed',
dbkey='hg18',
roles=[ str( admin_user_private_role.id ) ],
ldda_message=ldda_message,
strings_displayed=[ 'Upload files' ] )
global ldda8
ldda8 = get_latest_ldda_by_name( filename )
assert ldda8 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda8 from the database'
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_065_uploading_new_dataset_version(self):
"""Testing uploading a new version of a library dataset"""
# logged in as admin_user
filename = '4.bed'
ldda_message = 'Testing uploading a new version of a dataset'
self.upload_library_dataset(
cntrller='library_admin',
library_id=self.security.encode_id(library1.id),
folder_id=self.security.encode_id(subfolder1.id),
replace_id=self.security.encode_id(ldda4.library_dataset.id),
filename=filename,
file_type='auto',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=[
'Upload files',
'You are currently selecting a new file to replace'
])
global ldda4_version2
ldda4_version2 = get_latest_ldda_by_name(filename)
assert ldda4_version2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda4_version2 from the database'
self.ldda_edit_info(
'library_admin',
self.security.encode_id(library1.id),
self.security.encode_id(subfolder1.id),
self.security.encode_id(ldda4_version2.id),
ldda4_version2.name,
strings_displayed=[
'This is the latest version of this library dataset'
])
# Check the previous version
self.ldda_edit_info(
'library_admin',
self.security.encode_id(library1.id),
self.security.encode_id(subfolder1.id),
self.security.encode_id(ldda4.id),
ldda4.name,
strings_displayed=[
'This is an expired version of this library dataset'
])
# Make sure ldda4 is no longer displayed in the library
self.browse_library(cntrller='library_admin',
library_id=self.security.encode_id(library1.id),
strings_not_displayed=[ldda4.name, ldda4.message])
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_050_add_2nd_public_dataset_to_folder2(self):
"""Testing adding a 2nd public dataset folder2"""
# Logged in as admin_user
filename = '3.bed'
ldda_message = "Testing uploading %s" % filename
self.upload_library_dataset(
cntrller='library_admin',
library_id=self.security.encode_id(library1.id),
folder_id=self.security.encode_id(folder2.id),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=['Upload files'])
global ldda3
ldda3 = get_latest_ldda_by_name(filename)
assert ldda3 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda3 from the database'
self.browse_library(
cntrller='library_admin',
library_id=self.security.encode_id(library1.id),
strings_displayed=[ldda3.name, ldda3.message, 'bed'])
def test_055_copy_dataset_from_history_to_subfolder(self):
"""Testing copying a dataset from the current history to a subfolder"""
# logged in as admin_user
self.new_history()
filename = '4.bed'
self.upload_file(filename)
latest_hda = get_latest_hda()
self.upload_library_dataset(
cntrller='library_admin',
library_id=self.security.encode_id(library1.id),
folder_id=self.security.encode_id(subfolder1.id),
upload_option='import_from_history',
hda_ids=self.security.encode_id(latest_hda.id),
ldda_message='Imported from history',
strings_displayed=['Active datasets in your current history'])
global ldda4
ldda4 = get_latest_ldda_by_name(filename)
assert ldda4 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda4 from the database'
self.browse_library(
cntrller='library_admin',
library_id=self.security.encode_id(library1.id),
strings_displayed=[ldda4.name, ldda4.message, 'bed'])
def test_135_upload_unsorted_bam_to_library_using_file_path_with_link_to_file(
self):
"""Test uploading 3unsorted.bam, using filesystem_paths option in combination with link_to_files"""
filename = '3unsorted.bam'
self.upload_library_dataset(
cntrller='library_admin',
library_id=self.security.encode_id(library2.id),
folder_id=self.security.encode_id(library2.root_folder.id),
upload_option='upload_paths',
link_data_only='link_to_files',
filesystem_paths='test-data/3unsorted.bam')
global ldda8
ldda8 = get_latest_ldda_by_name(filename)
assert ldda8 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda8 from the database'
# The upload above should produce an error condition in the uploaded library dataset since
# the uploaded bam file is not sorted, and we are linking to the file.
self.ldda_info(cntrller='library_admin',
library_id=self.security.encode_id(library2.id),
folder_id=self.security.encode_id(
library2.root_folder.id),
ldda_id=self.security.encode_id(ldda8.id),
strings_displayed=[
'The uploaded files need grooming, so change your'
])
def test_120_populate_public_library2(self):
"""Testing library datasets within a library"""
# Logged in as admin_user
# Add a folder named Three to library2 root
root_folder = library2.root_folder
name = "One"
description = "One description"
self.add_folder('library_admin',
self.security.encode_id(library2.id),
self.security.encode_id(root_folder.id),
name=name,
description=description)
global folder3
folder3 = get_folder(root_folder.id, name, description)
assert folder3 is not None, 'Problem retrieving library folder named "%s" from the database' % name
# Upload dataset 1.bed to folder One
filename = '1.bed'
ldda_message = "Testing uploading %s" % filename
self.upload_library_dataset(
cntrller='library_admin',
library_id=self.security.encode_id(library2.id),
folder_id=self.security.encode_id(folder3.id),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=['Upload files'])
global ldda5
ldda5 = get_latest_ldda_by_name(filename)
assert ldda5 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda5 from the database'
# Add a sub-folder named Two to folder One
name = "Two"
description = "Two description"
self.add_folder('library_admin',
self.security.encode_id(library2.id),
self.security.encode_id(folder3.id),
name=name,
description=description)
global folder4
folder4 = get_folder(folder3.id, name, description)
assert folder4 is not None, 'Problem retrieving library folder named "%s" from the database' % name
# Upload dataset 2.bed to folder Two
filename = '2.bed'
ldda_message = "Testing uploading %s" % filename
self.upload_library_dataset(
cntrller='library_admin',
library_id=self.security.encode_id(library2.id),
folder_id=self.security.encode_id(folder4.id),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=['Upload files'])
global ldda6
ldda6 = get_latest_ldda_by_name(filename)
assert ldda6 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda6 from the database'
# Add a folder named Three to library2 root
name = "Three"
description = "Three description"
self.add_folder('library_admin',
self.security.encode_id(library2.id),
self.security.encode_id(root_folder.id),
name=name,
description=description)
global folder5
folder5 = get_folder(root_folder.id, name, description)
assert folder5 is not None, 'Problem retrieving library folder named "%s" from the database' % name
# Upload dataset 3.bed to library2 root folder
filename = '3.bed'
ldda_message = "Testing uploading %s" % filename
self.upload_library_dataset(
cntrller='library_admin',
library_id=self.security.encode_id(library2.id),
folder_id=self.security.encode_id(root_folder.id),
filename=filename,
file_type='bed',
dbkey='hg18',
ldda_message=ldda_message,
strings_displayed=['Upload files'])
global ldda7
ldda7 = get_latest_ldda_by_name(filename)
assert ldda7 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda7 from the database'
