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Source code for tool_shed.test.functional.test_1430_repair_installed_repository

import logging

from ..base.twilltestcase import (
    common,
    ShedTwillTestCase,
)

log = logging.getLogger(__name__)

category_name = "Test 1430 Repair installed repository"
category_description = "Test script 1430 for repairing an installed repository."
filter_repository_name = "filter_1430"
column_repository_name = "column_1430"
filter_repository_description = "Galaxy's filter tool for test 1430"
column_repository_description = "Add a value as a new column"
filter_repository_long_description = f"{filter_repository_name}: {filter_repository_description}"
column_repository_long_description = f"{column_repository_name}: {column_repository_description}"

"""
In the Tool Shed:

1) Create and populate the filter_1430 repository

2) Create and populate the column_1430 repository

3) Upload a repository_dependencies.xml file to the column_1430 repository that creates a repository dependency on the filter_1430 repository.

In Galaxy:

1) Install the column_1430 repository, making sure to check the checkbox to Handle repository dependencies so that the filter
   repository is also installed. Make sure to install the repositories in a specified section of the tool panel.

2) Uninstall the filter_1430 repository.
"""


[docs]class TestRepairRepository(ShedTwillTestCase): """Test repairing an installed repository."""
[docs] def test_0000_initiate_users_and_category(self): """Create necessary user accounts and login as an admin user.""" self.login(email=common.admin_email, username=common.admin_username) self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_2_email, username=common.test_user_2_name) self.login(email=common.test_user_1_email, username=common.test_user_1_name)
[docs] def test_0005_create_filter_repository(self): """Create and populate the filter_1430 repository. This is step 1 - Create and populate the filter_1430 repository. This repository will be depended on by the column_1430 repository. """ category = self.populator.get_category_with_name(category_name) 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=[], ) 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="Populate filter_1430 with version 1.1.0.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0010_create_column_repository(self): """Create and populate the column_1430 repository. This is step 2 - Create and populate the column_1430 repository. This repository will depend on the filter_1430 repository. """ category = self.populator.get_category_with_name(category_name) 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=[], ) 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="Populate column_1430 with tool definitions.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0015_create_repository_dependency(self): """Create a dependency on filter_1430. This is step 3 - Upload a repository_dependencies.xml file to the column_1430 repository that creates a repository dependency on the filter_1430 repository. """ column_repository = self.test_db_util.get_repository_by_name_and_owner("column_1430", common.test_user_1_name) filter_repository = self.test_db_util.get_repository_by_name_and_owner("filter_1430", common.test_user_1_name) tool_shed_url = self.url name = filter_repository.name owner = filter_repository.user.username changeset_revision = self.get_repository_tip(filter_repository) repository_dependency_tuple = (tool_shed_url, name, owner, changeset_revision) filepath = self.generate_temp_path("1430_repository_dependency") self.create_repository_dependency(column_repository, [repository_dependency_tuple], filepath=filepath)
[docs] def test_0020_install_column_repository(self): """Install the column_1430 repository into Galaxy. This is step 1 (galaxy side) - Install the column_1430 repository, making sure to check the checkbox to handle repository dependencies so that the filter_1430 repository is also installed. Make sure to install the repositories in a specified section of the tool panel. """ self.galaxy_login(email=common.admin_email, username=common.admin_username) post_submit_strings_displayed = ["column_1430", "filter_1430"] self.install_repository( "column_1430", common.test_user_1_name, category_name, new_tool_panel_section_label="repair", post_submit_strings_displayed=post_submit_strings_displayed, install_tool_dependencies=False, install_repository_dependencies=True, )
[docs] def test_0025_uninstall_filter_repository(self): """Uninstall the filter_1430 repository from Galaxy. This is step 2 - Uninstall the filter_1430 repository. """ installed_repository = self.test_db_util.get_installed_repository_by_name_owner( "filter_1430", common.test_user_1_name ) strings_displayed = ["Uninstalling this repository will result in the following"] strings_not_displayed = [] self.uninstall_repository( installed_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) strings_not_displayed = [ "filter_1430", "Galaxy's filter tool for test 1430", installed_repository.installed_changeset_revision, ] self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)