import os
from ..base.twilltestcase import (
common,
ShedTwillTestCase,
)
[docs]class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
"""Test uninstalling and reinstalling a repository with tool dependencies."""
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
self.test_db_util.get_galaxy_private_role(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
), f"Problem retrieving user with email {common.test_user_1_email} from the database"
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, f"Problem retrieving user with email {common.admin_email} from the database"
self.test_db_util.get_private_role(admin_user)
[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_id=self.security.encode_id(category.id),
)
if self.repository_is_new(repository):
self.upload_file(
repository,
filename="freebayes/freebayes.xml",
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded the tool xml.",
strings_displayed=[
"Metadata may have been defined",
"This file requires an entry",
"tool_data_table_conf",
],
strings_not_displayed=[],
)
self.upload_file(
repository,
filename="freebayes/tool_data_table_conf.xml.sample",
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded the tool data table sample file.",
strings_displayed=[],
strings_not_displayed=[],
)
self.upload_file(
repository,
filename="freebayes/sam_fa_indices.loc.sample",
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded tool data table .loc file.",
strings_displayed=[],
strings_not_displayed=[],
)
self.upload_file(
repository,
filename=os.path.join("freebayes", "malformed_tool_dependencies", "tool_dependencies.xml"),
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded malformed tool dependency XML.",
strings_displayed=["Exception attempting to parse", "not well-formed"],
strings_not_displayed=[],
)
self.upload_file(
repository,
filename=os.path.join("freebayes", "invalid_tool_dependencies", "tool_dependencies.xml"),
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded invalid tool dependency XML.",
strings_displayed=[
"The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration"
],
strings_not_displayed=[],
)
self.upload_file(
repository,
filename=os.path.join("freebayes", "tool_dependencies.xml"),
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded valid tool dependency XML.",
strings_displayed=[],
strings_not_displayed=[],
)
[docs] def test_0010_install_freebayes_repository(self):
"""Install the freebayes repository into the Galaxy instance."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
strings_displayed = []
self.install_repository(
"freebayes_0010",
common.test_user_1_name,
"Test 0010 Repository With Tool Dependencies",
strings_displayed=strings_displayed,
new_tool_panel_section_label="test_1210",
)
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
"freebayes_0010", common.test_user_1_name
)
strings_displayed = [
"freebayes_0010",
"Galaxy's freebayes tool",
"user1",
self.url.replace("http://", ""),
installed_repository.installed_changeset_revision,
]
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
[docs] def test_0015_uninstall_freebayes_repository(self):
"""Uninstall the freebayes repository."""
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
"freebayes_0010", common.test_user_1_name
)
self.uninstall_repository(installed_repository)
strings_not_displayed = [installed_repository.name, installed_repository.installed_changeset_revision]
self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
[docs] def test_0020_reinstall_freebayes_repository(self):
"""Reinstall the freebayes repository."""
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
"freebayes_0010", common.test_user_1_name
)
self.reinstall_repository(installed_repository)
strings_displayed = [
"freebayes_0010",
"Galaxy's freebayes tool",
"user1",
self.url.replace("http://", ""),
installed_repository.installed_changeset_revision,
]
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
strings_displayed.extend(["Installed tool shed repository", "Valid tools", "FreeBayes"])
self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
self.verify_tool_metadata_for_installed_repository(installed_repository)
[docs] def test_0025_deactivate_freebayes_repository(self):
"""Deactivate the freebayes repository without removing it from disk."""
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
"freebayes_0010", common.test_user_1_name
)
self.deactivate_repository(installed_repository)
strings_not_displayed = [installed_repository.name, installed_repository.installed_changeset_revision]
self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
[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.test_db_util.get_installed_repository_by_name_owner(
"freebayes_0010", common.test_user_1_name
)
self.reactivate_repository(installed_repository)
strings_displayed = [
"freebayes_0010",
"Galaxy's freebayes tool",
"user1",
self.url.replace("http://", ""),
installed_repository.installed_changeset_revision,
]
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
strings_displayed.extend(["Installed tool shed repository", "Valid tools", "FreeBayes"])
self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
self.verify_tool_metadata_for_installed_repository(installed_repository)