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)
        admin_user = self.test_db_util.get_galaxy_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_galaxy_private_role(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_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_id=self.security.encode_id(category.id))
        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 = ['install Tool Shed managed', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18']
        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)