Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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) 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_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=category, 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=category, 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=category, 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._get_repository_by_name_and_owner(filter_repository_name, common.test_user_1_name) column_repository = self._get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name) convert_repository = self._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.owner, column_revision) convert_tuple = (self.url, convert_repository.name, convert_repository.owner, convert_revision) filter_tuple = (self.url, filter_repository.name, filter_repository.owner, 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._get_repository_by_name_and_owner(filter_repository_name, common.test_user_1_name) column_repository = self._get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name) convert_repository = self._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._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)] 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, )
[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"