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Source code for tool_shed.test.functional.test_1150_datatype_converters
from ..base.twilltestcase import common, ShedTwillTestCase
repository_name = 'bed_to_gff_0130'
repository_description = "Converter: BED to GFF"
repository_long_description = "Convert bed to gff"
category_name = 'Test 0130 Datatype Converters'
category_description = 'Test 0130 Datatype Converters'
'''
1) Install the bed_to_gff_converter repository.
2) Make sure the page section to select a tool panel section is NOT displayed since the tool will not be displayed in the Galaxy tool panel.
3) Make sure the bed_to_gff_converter tool is not displayed in the tool panel.
'''
[docs]class TestDatatypeConverters(ShedTwillTestCase):
'''Test features related to datatype converters.'''
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email
self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
admin_user = self.test_db_util.get_user(common.admin_email)
assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
self.test_db_util.get_private_role(admin_user)
[docs] def test_0005_create_bed_to_gff_repository(self):
'''Create and populate bed_to_gff_0130.'''
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
# Create a repository named bed_to_gff_0130 owned by user1.
repository = self.get_or_create_repository(name=repository_name,
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
if self.repository_is_new(repository):
# Upload bed_to_gff_converter.tar to the repository, if the repository is new.
self.upload_file(repository,
filename='bed_to_gff_converter/bed_to_gff_converter.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded bed_to_gff_converter.tar.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0010_install_datatype_converter_to_galaxy(self):
'''Install bed_to_gff_converter_0130 into the running Galaxy instance.'''
'''
We are at step 1 - Install the bed_to_gff_converter repository.
Install bed_to_gff_converter_0130, checking that the option to select the tool panel section is *not* displayed.
'''
self.galaxy_login(email=common.admin_email, username=common.admin_username)
repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
preview_strings_displayed = [repository.name, self.get_repository_tip(repository)]
strings_displayed = ['Your Galaxy instance is configured with', 'shed-related tool configuration file']
strings_not_displayed = ['tool panel section']
self.install_repository(repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
preview_strings_displayed=preview_strings_displayed,
strings_displayed=strings_displayed,
strings_not_displayed=strings_not_displayed,
post_submit_strings_displayed=[repository.name, 'New'],
includes_tools_for_display_in_tool_panel=False)
[docs] def test_0015_uninstall_and_verify_tool_panel_section(self):
'''Uninstall bed_to_gff_converter_0130 and verify that the saved tool_panel_section is None.'''
'''
We are at step 3 - Make sure the bed_to_gff_converter tool is not displayed in the tool panel.
The previous tool panel section for a tool is only recorded in the metadata when a repository is uninstalled,
so we have to uninstall it first, then verify that it was not assigned a tool panel section.
'''
repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
self.uninstall_repository(repository)
self.verify_installed_repository_no_tool_panel_section(repository)