Source code for tool_shed.test.functional.test_1000_install_basic_repository

from ..base.twilltestcase import common, ShedTwillTestCase


[docs]class BasicToolShedFeatures(ShedTwillTestCase):
    '''Test installing a basic repository.'''

[docs]    def test_0000_initiate_users(self):
        """Create necessary user accounts."""
        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)
        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)

[docs]    def test_0005_ensure_repositories_and_categories_exist(self):
        '''Create the 0000 category and upload the filtering repository to it, if necessary.'''
        self.login(email=common.admin_email, username=common.admin_username)
        category = self.create_category(name='Test 0000 Basic Repository Features 2', description='Test Description 0000 Basic Repository Features 2')
        category = self.create_category(name='Test 0000 Basic Repository Features 1', description='Test Description 0000 Basic Repository Features 1')
        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
        repository = self.get_or_create_repository(name='filtering_0000',
                                                   description="Galaxy's filtering tool",
                                                   long_description="Long description of Galaxy's filtering 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='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=[])
            self.upload_file(repository,
                             filename='filtering/filtering_0000.txt',
                             filepath=None,
                             valid_tools_only=True,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded readme for 1.1.0',
                             strings_displayed=[],
                             strings_not_displayed=[])
            self.upload_file(repository,
                             filename='filtering/filtering_2.2.0.tar',
                             filepath=None,
                             valid_tools_only=True,
                             uncompress_file=True,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded filtering 2.2.0 tarball.',
                             strings_displayed=[],
                             strings_not_displayed=[])
            self.upload_file(repository,
                             filename='readme.txt',
                             filepath=None,
                             valid_tools_only=True,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded readme for 2.2.0',
                             strings_displayed=[],
                             strings_not_displayed=[])

[docs]    def test_0010_browse_tool_sheds(self):
        """Browse the available tool sheds in this Galaxy instance."""
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        self.browse_tool_shed(url=self.url, strings_displayed=['Test 0000 Basic Repository Features 1', 'Test 0000 Basic Repository Features 2'])

[docs]    def test_0015_browse_test_0000_category(self):
        '''Browse the category created in test 0000. It should contain the filtering_0000 repository also created in that test.'''
        category = self.test_db_util.get_category_by_name('Test 0000 Basic Repository Features 1')
        self.browse_category(category, strings_displayed=['filtering_0000'])

[docs]    def test_0020_preview_filtering_repository(self):
        '''Load the preview page for the filtering_0000 repository in the tool shed.'''
        self.preview_repository_in_tool_shed('filtering_0000', common.test_user_1_name, strings_displayed=['filtering_0000', 'Valid tools'])

[docs]    def test_0025_install_filtering_repository(self):
        self.install_repository('filtering_0000',
                                common.test_user_1_name,
                                'Test 0000 Basic Repository Features 1',
                                new_tool_panel_section_label='test_1000')
        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_0000', common.test_user_1_name)
        strings_displayed = ['filtering_0000',
                             "Galaxy's filtering tool",
                             'user1',
                             self.url.replace('http://', ''),
                             str(installed_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(installed_repository, strings_displayed=strings_displayed)
        self.verify_tool_metadata_for_installed_repository(installed_repository)

[docs]    def test_0030_install_filtering_repository_again(self):
        '''Attempt to install the already installed filtering repository.'''
        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('filtering_0000', common.test_user_1_name)
        # The page displayed after installation is the ajaxian "Montior installing tool shed repositories" page.  Since the filter
        # repository was already installed, nothing will be in the process of being installed, so the grid will not display 'filtering_0000'.
        post_submit_strings_not_displayed = ['filtering_0000']
        self.install_repository('filtering_0000',
                                common.test_user_1_name,
                                'Test 0000 Basic Repository Features 1',
                                post_submit_strings_not_displayed=post_submit_strings_not_displayed)
        strings_displayed = ['filtering_0000',
                             "Galaxy's filtering tool",
                             'user1',
                             self.url.replace('http://', ''),
                             str(installed_repository.installed_changeset_revision)]
        self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
        self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)

[docs]    def test_0035_verify_installed_repository_metadata(self):
        '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
        self.verify_installed_repository_metadata_unchanged('filtering_0000', common.test_user_1_name)