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Source code for tool_shed.test.functional.test_1090_repository_dependency_handling

import logging

from ..base.twilltestcase import common, ShedTwillTestCase

column_repository_name = 'column_maker_1085'
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"

convert_repository_name = 'convert_chars_1085'
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"

category_name = 'Test 1085 Advanced Circular Dependencies'
category_description = 'Test circular dependency features'

log = logging.getLogger(__name__)


[docs]class TestRepositoryDependencies(ShedTwillTestCase): '''Testing the behavior of repository dependencies with tool panel sections.'''
[docs] def test_0000_create_or_login_admin_user(self): """Create necessary user accounts and login as an admin user.""" 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, 'Problem retrieving user with email %s from the database' % common.admin_email 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, 'Problem retrieving user with email %s from the database' % common.test_user_1_email 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, 'Problem retrieving user with email %s from the database' % common.admin_email self.test_db_util.get_private_role(admin_user)
[docs] def test_0005_create_and_populate_column_repository(self): """Create a category for this test suite and add repositories to it.""" 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=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 self.repository_is_new(repository): 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_0010_create_and_populate_convert_repository(self): self.login(email=common.admin_email, username=common.admin_username) 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): 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_0015_create_and_upload_dependency_files(self): convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_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) repository_dependencies_path = self.generate_temp_path('test_1085', additional_paths=['column']) repository_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository)) self.create_repository_dependency(repository=column_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path) repository_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository)) self.create_repository_dependency(repository=convert_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
[docs] def test_0020_install_repositories(self): '''Install column_maker into column_maker tool panel section and install repository dependencies.''' self.galaxy_login(email=common.admin_email, username=common.admin_username) self.install_repository(column_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label='column_maker', strings_displayed=['install_repository_dependencies']) installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name, common.test_user_1_name) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name) browse_strings_displayed = ['convert_chars_1085', 'Convert delimiters', self.url.replace('http://', ''), installed_convert_repository.installed_changeset_revision, 'column_maker_1085', 'Add column', installed_column_repository.installed_changeset_revision] strings_displayed = ['convert_chars_1085', 'Convert delimiters', self.url.replace('http://', ''), installed_convert_repository.installed_changeset_revision, 'column_maker_1085', installed_column_repository.installed_changeset_revision, 'Installed repository dependencies'] self.display_galaxy_browse_repositories_page(strings_displayed=browse_strings_displayed) self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
[docs] def test_0025_uninstall_column_repository(self): '''uninstall column_maker, verify same section''' installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name) self.uninstall_repository(installed_column_repository) self.test_db_util.ga_refresh(installed_column_repository) self.check_galaxy_repository_tool_panel_section(installed_column_repository, 'column_maker')
[docs] def test_0030_uninstall_convert_repository(self): installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name, common.test_user_1_name) self.uninstall_repository(installed_convert_repository) self.test_db_util.ga_refresh(installed_convert_repository) self.check_galaxy_repository_tool_panel_section(installed_convert_repository, 'column_maker')
[docs] def test_0035_reinstall_column_repository(self): '''reinstall column_maker into new section 'new_column_maker' (no_changes = false), no dependencies''' installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name) self.reinstall_repository(installed_column_repository, install_tool_dependencies=False, install_repository_dependencies=False, new_tool_panel_section_label='new_column_maker', no_changes=False) strings_displayed = ['column_maker_1085', 'Add column', self.url.replace('http://', ''), installed_column_repository.installed_changeset_revision] self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
[docs] def test_0040_reinstall_convert_repository(self): '''reinstall convert_chars into new section 'new_convert_chars' (no_changes = false), no dependencies''' installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name, common.test_user_1_name) self.reinstall_repository(installed_convert_repository, install_tool_dependencies=False, install_repository_dependencies=False, new_tool_panel_section_label='new_convert_chars', no_changes=False) strings_displayed = ['convert_chars_1085', 'Convert delimiters', self.url.replace('http://', ''), installed_convert_repository.installed_changeset_revision] self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
# The following check fails somewhere around 5% of the time maybe on Jenkins. # https://jenkins.galaxyproject.org/job/docker-toolshed/5578/ # https://jenkins.galaxyproject.org/job/docker-toolshed/5198/ # def test_0045_uninstall_and_verify_tool_panel_sections( self ): # '''uninstall both and verify tool panel sections''' # installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, # common.test_user_1_name ) # installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, # common.test_user_1_name ) # self.uninstall_repository( installed_convert_repository ) # self.uninstall_repository( installed_column_repository ) # self.test_db_util.ga_refresh( installed_convert_repository ) # self.test_db_util.ga_refresh( installed_column_repository ) # self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'new_column_maker' ) # self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'new_convert_chars' )