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Source code for tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies
import os
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
[docs]class TestUninstallingAndReinstallingRepositories(ShedTwillTestCase):
"""Test uninstalling and reinstalling a repository with tool dependencies."""
requires_galaxy = True
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
self.login(email=common.admin_email, username=common.admin_username)
[docs] def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0010 category and upload the freebayes repository to the tool shed, if necessary."""
category = self.create_category(
name="Test 0010 Repository With Tool Dependencies",
description="Tests for a repository with tool dependencies.",
)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(
name="freebayes_0010",
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category=category,
)
if self.repository_is_new(repository):
strings_displayed = [
"Metadata may have been defined",
"This file requires an entry",
"tool_data_table_conf",
]
self.add_file_to_repository(repository, "freebayes/freebayes.xml", strings_displayed=strings_displayed)
strings_displayed = ["Upload a file named <b>sam_fa_indices.loc.sample"]
self.add_file_to_repository(
repository, "freebayes/tool_data_table_conf.xml.sample", strings_displayed=strings_displayed
)
self.add_file_to_repository(repository, "freebayes/sam_fa_indices.loc.sample")
target = os.path.join("freebayes", "malformed_tool_dependencies", "tool_dependencies.xml")
self.add_file_to_repository(
repository, target, strings_displayed=["Exception attempting to parse", "invalid element name"]
)
target = os.path.join("freebayes", "invalid_tool_dependencies", "tool_dependencies.xml")
strings_displayed = [
"The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration"
]
self.add_file_to_repository(repository, target, strings_displayed=strings_displayed)
target = os.path.join("freebayes", "tool_dependencies.xml")
self.add_file_to_repository(repository, target)
[docs] def test_0010_install_freebayes_repository(self):
"""Install the freebayes repository into the Galaxy instance."""
self._install_repository(
"freebayes_0010",
common.test_user_1_name,
"Test 0010 Repository With Tool Dependencies",
new_tool_panel_section_label="test_1210",
)
self._assert_has_installed_repos_with_names("freebayes_0010")
[docs] def test_0015_uninstall_freebayes_repository(self):
"""Uninstall the freebayes repository."""
installed_repository = self._get_installed_repository_by_name_owner("freebayes_0010", common.test_user_1_name)
self._uninstall_repository(installed_repository)
self._assert_has_no_installed_repos_with_names("freebayes_0010")
[docs] def test_0020_reinstall_freebayes_repository(self):
"""Reinstall the freebayes repository."""
installed_repository = self._get_installed_repository_by_name_owner("freebayes_0010", common.test_user_1_name)
self.reinstall_repository_api(installed_repository)
self._assert_has_installed_repos_with_names("freebayes_0010")
self._assert_has_valid_tool_with_name("FreeBayes")
self._assert_repo_has_tool_with_id(installed_repository, "freebayes")
[docs] def test_0025_deactivate_freebayes_repository(self):
"""Deactivate the freebayes repository without removing it from disk."""
installed_repository = self._get_installed_repository_by_name_owner("freebayes_0010", common.test_user_1_name)
self.deactivate_repository(installed_repository)
self._assert_has_no_installed_repos_with_names("freebayes_0010")
[docs] def test_0030_reactivate_freebayes_repository(self):
"""Reactivate the freebayes repository and verify that it now shows up in the list of installed repositories."""
installed_repository = self._get_installed_repository_by_name_owner("freebayes_0010", common.test_user_1_name)
self.reactivate_repository(installed_repository)
self._assert_has_installed_repos_with_names("freebayes_0010")
self._assert_has_valid_tool_with_name("FreeBayes")
self._assert_repo_has_tool_with_id(installed_repository, "freebayes")