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Source code for tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies

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) 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): 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)