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Source code for tool_shed.test.functional.test_0070_invalid_tool
from ..base.twilltestcase import common, ShedTwillTestCase
repository_name = 'bismark_0070'
repository_description = "Galaxy's bismark wrapper"
repository_long_description = "Long description of Galaxy's bismark wrapper"
category_name = 'Test 0070 Invalid Tool Revisions'
category_description = 'Tests for a repository with invalid tool revisions.'
[docs]class TestBismarkRepository(ShedTwillTestCase):
'''Testing bismark with valid and invalid tool entries.'''
[docs] def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an 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_category_and_repository(self):
"""Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool."""
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
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=[])
self.upload_file(repository,
filename='bismark/bismark.tar',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded bismark tarball.',
strings_displayed=[],
strings_not_displayed=[])
self.display_manage_repository_page(repository, strings_displayed=['Invalid tools'])
invalid_revision = self.get_repository_tip(repository)
self.upload_file(repository,
filename='bismark/bismark_methylation_extractor.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded an updated tool xml.',
strings_displayed=[],
strings_not_displayed=[])
valid_revision = self.get_repository_tip(repository)
self.test_db_util.refresh(repository)
tool_guid = '%s/repos/user1/bismark_0070/bismark_methylation_extractor/0.7.7.3' % self.url.replace('http://', '').rstrip('/')
tool_metadata_strings_displayed = [tool_guid,
'0.7.7.3', # The tool version.
'bismark_methylation_extractor', # The tool ID.
'Bismark', # The tool name.
'methylation extractor'] # The tool description.
tool_page_strings_displayed = ['Bismark (version 0.7.7.3)']
self.check_repository_tools_for_changeset_revision(repository,
valid_revision,
tool_metadata_strings_displayed=tool_metadata_strings_displayed,
tool_page_strings_displayed=tool_page_strings_displayed)
self.check_repository_invalid_tools_for_changeset_revision(repository, invalid_revision)