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)
        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.create_category(name=category_name, description=category_description)
        self.login(email=common.test_user_2_email, username=common.test_user_2_name)
        test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
        assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email
        self.test_db_util.get_private_role(test_user_2)
        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)

[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.test_db_util.get_category_by_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_id=self.security.encode_id(category.id),
                                                   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.test_db_util.get_category_by_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_id=self.security.encode_id(category.id),
                                                   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)