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Source code for tool_shed.test.functional.test_1180_circular_prior_installation_required
import logging
from ..base.twilltestcase import (
common,
ShedTwillTestCase,
)
log = logging.getLogger(__name__)
filter_repository_name = "filtering_0160"
filter_repository_description = "Galaxy's filtering tool for test 0160"
filter_repository_long_description = "Long description of Galaxy's filtering tool for test 0160"
column_repository_name = "column_maker_0160"
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"
convert_repository_name = "convert_chars_0160"
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"
category_name = "Test 0160 Simple Prior Installation"
category_description = "Test 0160 Simple Prior Installation"
"""
Create column_maker, filtering, and convert_chars.
Column maker repository dependency:
<repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />
<repository toolshed="self.url" name="filtering" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />
Convert chars repository dependency:
<repository toolshed="self.url" name="column_maker" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />
<repository toolshed="self.url" name="filtering" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />
Filtering repository dependency:
<repository toolshed="self.url" name="column_maker" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />
<repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />
Verify display.
Galaxy side:
Install filtering.
Verify that convert_chars was installed first, contrary to the ordering that would be present without prior_installation_required.
"""
running_standalone = False
[docs]class TestSimplePriorInstallation(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
), f"Problem retrieving user with email {common.admin_email} from the database"
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
), 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_create_convert_repository(self):
"""Create and populate convert_chars_0160."""
global running_standalone
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=convert_repository_name,
description=convert_repository_description,
long_description=convert_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):
running_standalone = True
self.upload_file(
repository,
filename="convert_chars/convert_chars.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded convert_chars tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
[docs] def test_0010_create_column_repository(self):
"""Create and populate convert_chars_0160."""
global running_standalone
category = self.create_category(name=category_name, description=category_description)
repository = self.get_or_create_repository(
name=column_repository_name,
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[],
)
if running_standalone:
self.upload_file(
repository,
filename="column_maker/column_maker.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded column_maker tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
[docs] def test_0015_create_filtering_repository(self):
"""Create and populate filtering_0160."""
global running_standalone
category = self.create_category(name=category_name, description=category_description)
repository = self.get_or_create_repository(
name=filter_repository_name,
description=filter_repository_description,
long_description=filter_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[],
)
if running_standalone:
self.upload_file(
repository,
filename="filtering/filtering_1.1.0.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded filtering 1.1.0 tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
[docs] def test_0020_create_repository_dependency(self):
"""Create a repository dependency specifying convert_chars.
Each of the three repositories should depend on the other two, to make this as circular as possible.
"""
global running_standalone
filter_repository = self.test_db_util.get_repository_by_name_and_owner(
filter_repository_name, common.test_user_1_name
)
column_repository = self.test_db_util.get_repository_by_name_and_owner(
column_repository_name, common.test_user_1_name
)
convert_repository = self.test_db_util.get_repository_by_name_and_owner(
convert_repository_name, common.test_user_1_name
)
filter_revision = self.get_repository_tip(filter_repository)
column_revision = self.get_repository_tip(column_repository)
convert_revision = self.get_repository_tip(convert_repository)
if running_standalone:
dependency_xml_path = self.generate_temp_path("test_1160", additional_paths=["column"])
column_tuple = (self.url, column_repository.name, column_repository.user.username, column_revision)
convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, convert_revision)
filter_tuple = (self.url, filter_repository.name, filter_repository.user.username, filter_revision)
self.create_repository_dependency(
repository=column_repository,
repository_tuples=[convert_tuple, filter_tuple],
filepath=dependency_xml_path,
prior_installation_required=False,
)
self.create_repository_dependency(
repository=convert_repository,
repository_tuples=[column_tuple, filter_tuple],
filepath=dependency_xml_path,
prior_installation_required=False,
)
self.create_repository_dependency(
repository=filter_repository,
repository_tuples=[convert_tuple, column_tuple],
filepath=dependency_xml_path,
prior_installation_required=True,
)
[docs] def test_0025_verify_repository_dependency(self):
"""Verify that the previously generated repositiory dependency displays correctly."""
filter_repository = self.test_db_util.get_repository_by_name_and_owner(
filter_repository_name, common.test_user_1_name
)
column_repository = self.test_db_util.get_repository_by_name_and_owner(
column_repository_name, common.test_user_1_name
)
convert_repository = self.test_db_util.get_repository_by_name_and_owner(
convert_repository_name, common.test_user_1_name
)
self.check_repository_dependency(
repository=column_repository,
depends_on_repository=convert_repository,
depends_on_changeset_revision=None,
changeset_revision=None,
)
self.check_repository_dependency(
repository=column_repository,
depends_on_repository=filter_repository,
depends_on_changeset_revision=None,
changeset_revision=None,
)
self.check_repository_dependency(
repository=convert_repository,
depends_on_repository=column_repository,
depends_on_changeset_revision=None,
changeset_revision=None,
)
self.check_repository_dependency(
repository=convert_repository,
depends_on_repository=filter_repository,
depends_on_changeset_revision=None,
changeset_revision=None,
)
self.check_repository_dependency(
repository=filter_repository,
depends_on_repository=column_repository,
depends_on_changeset_revision=None,
changeset_revision=None,
)
self.check_repository_dependency(
repository=filter_repository,
depends_on_repository=convert_repository,
depends_on_changeset_revision=None,
changeset_revision=None,
)
[docs] def test_0030_install_filtering_repository(self):
"""Install the filtering_0160 repository."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
filter_repository = self.test_db_util.get_repository_by_name_and_owner(
filter_repository_name, common.test_user_1_name
)
preview_strings_displayed = ["filtering_0160", self.get_repository_tip(filter_repository)]
strings_displayed = ["Choose the tool panel section"]
self.install_repository(
filter_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
preview_strings_displayed=preview_strings_displayed,
strings_displayed=strings_displayed,
strings_not_displayed=[],
post_submit_strings_displayed=["filtering_0160", "New"],
includes_tools_for_display_in_tool_panel=True,
)
[docs] def test_0035_verify_installation_order(self):
"""Verify that convert_chars_0160 and column_maker_0160 were installed before filtering_0160."""
filter_repository = self.test_db_util.get_installed_repository_by_name_owner(
filter_repository_name, common.test_user_1_name
)
column_repository = self.test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name
)
convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name
)
# Filtering was selected for installation, so convert chars and column maker should have been installed first.
assert (
filter_repository.update_time > convert_repository.update_time
), "Error: convert_chars_0160 shows a later update time than filtering_0160"
assert (
filter_repository.update_time > column_repository.update_time
), "Error: column_maker_0160 shows a later update time than filtering_0160"
[docs] def test_0040_deactivate_all_repositories(self):
"""Uninstall convert_chars_0160, column_maker_0160, and filtering_0160."""
filter_repository = self.test_db_util.get_installed_repository_by_name_owner(
filter_repository_name, common.test_user_1_name
)
column_repository = self.test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name
)
convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name
)
self.deactivate_repository(filter_repository)
self.deactivate_repository(column_repository)
self.deactivate_repository(convert_repository)
[docs] def test_0045_reactivate_filter_repository(self):
"""Reinstall the filtering_0160 repository."""
filter_repository = self.test_db_util.get_installed_repository_by_name_owner(
filter_repository_name, common.test_user_1_name
)
self.reactivate_repository(filter_repository)
strings_displayed = [
"filtering_0160",
"Galaxy's filtering tool for test 0160",
"user1",
self.url.replace("http://", ""),
filter_repository.installed_changeset_revision,
]
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
strings_displayed.extend(["Installed tool shed repository", "Valid tools", "Filter1"])
self.display_installed_repository_manage_page(filter_repository, strings_displayed=strings_displayed)
self.verify_tool_metadata_for_installed_repository(filter_repository)
[docs] def test_0050_verify_reinstallation_order(self):
"""Verify that convert_chars_0160 and column_maker_0160 were reinstalled before filtering_0160."""
# Fixme: this test is not covering any important behavior since repositories were only deactivated and not uninstalled.
filter_repository = self.test_db_util.get_installed_repository_by_name_owner(
filter_repository_name, common.test_user_1_name
)
column_repository = self.test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name
)
convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
convert_repository_name, common.test_user_1_name
)
# Filtering was selected for reinstallation, so convert chars and column maker should have been installed first.
for repo in [convert_repository, column_repository, filter_repository]:
self.test_db_util.install_session.refresh(repo)
assert (
filter_repository.update_time > convert_repository.update_time
), "Prior installed convert_chars_0160 shows a later update time than filtering_0160"
assert (
filter_repository.update_time > column_repository.update_time
), "Prior installed column_maker_0160 shows a later update time than filtering_0160"