Source code for tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies

from ..base.twilltestcase import common, ShedTwillTestCase

datatypes_repository_name = 'emboss_datatypes_0110'
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."

emboss_repository_name = 'emboss_0110'
emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'

category_name = 'Test 0110 Invalid Repository Dependencies'
category_desc = 'Test 0110 Invalid Repository Dependencies'


[docs]class TestBasicRepositoryDependencies(ShedTwillTestCase):
    '''Testing emboss 5 with repository dependencies.'''

[docs]    def test_0000_initiate_users(self):
        """Create necessary user accounts and login as an 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_category(self):
        """Create a category for this test suite"""
        self.create_category(name=category_name, description=category_desc)

[docs]    def test_0010_create_emboss_datatypes_repository_and_upload_tarball(self):
        '''Create and populate the emboss_datatypes repository.'''
        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
        category = self.test_db_util.get_category_by_name(category_name)
        repository = self.get_or_create_repository(name=datatypes_repository_name,
                                             description=datatypes_repository_description,
                                             long_description=datatypes_repository_long_description,
                                             owner=common.test_user_1_name,
                                             category_id=self.security.encode_id(category.id),
                                             strings_displayed=[])
        self.upload_file(repository,
                         filename='emboss/datatypes/datatypes_conf.xml',
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded datatypes_conf.xml.',
                         strings_displayed=[],
                         strings_not_displayed=[])

[docs]    def test_0015_verify_datatypes_in_datatypes_repository(self):
        '''Verify that the emboss_datatypes repository contains datatype entries.'''
        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
        self.display_manage_repository_page(repository, strings_displayed=['Datatypes', 'equicktandem', 'hennig86', 'vectorstrip'])

[docs]    def test_0020_create_emboss_5_repository_and_upload_files(self):
        '''Create and populate the emboss_5_0110 repository.'''
        category = self.test_db_util.get_category_by_name(category_name)
        repository = self.get_or_create_repository(name=emboss_repository_name,
                                             description=emboss_repository_description,
                                             long_description=emboss_repository_long_description,
                                             owner=common.test_user_1_name,
                                             category_id=self.security.encode_id(category.id),
                                             strings_displayed=[])
        self.upload_file(repository,
                         filename='emboss/emboss.tar',
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded emboss tool tarball.',
                         strings_displayed=[],
                         strings_not_displayed=[])

[docs]    def test_0025_generate_repository_dependency_with_invalid_url(self):
        '''Generate a repository dependency for emboss 5 with an invalid URL.'''
        dependency_path = self.generate_temp_path('test_0110', additional_paths=['simple'])
        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
        url = 'http://http://this is not an url!'
        name = datatypes_repository.name
        owner = datatypes_repository.user.username
        changeset_revision = self.get_repository_tip(datatypes_repository)
        strings_displayed = ['Repository dependencies are currently supported only within the same tool shed']
        repository_tuple = (url, name, owner, changeset_revision)
        self.create_repository_dependency(repository=emboss_repository,
                                          filepath=dependency_path,
                                          repository_tuples=[repository_tuple],
                                          strings_displayed=strings_displayed,
                                          complex=False)

[docs]    def test_0030_generate_repository_dependency_with_invalid_name(self):
        '''Generate a repository dependency for emboss 5 with an invalid name.'''
        dependency_path = self.generate_temp_path('test_0110', additional_paths=['simple'])
        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
        url = self.url
        name = '!?invalid?!'
        owner = repository.user.username
        changeset_revision = self.get_repository_tip(repository)
        strings_displayed = ['because the name is invalid.']
        repository_tuple = (url, name, owner, changeset_revision)
        self.create_repository_dependency(repository=emboss_repository,
                                          filepath=dependency_path,
                                          repository_tuples=[repository_tuple],
                                          strings_displayed=strings_displayed,
                                          complex=False)

[docs]    def test_0035_generate_repository_dependency_with_invalid_owner(self):
        '''Generate a repository dependency for emboss 5 with an invalid owner.'''
        dependency_path = self.generate_temp_path('test_0110', additional_paths=['simple'])
        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
        url = self.url
        name = repository.name
        owner = '!?invalid?!'
        changeset_revision = self.get_repository_tip(repository)
        strings_displayed = ['because the owner is invalid.']
        repository_tuple = (url, name, owner, changeset_revision)
        self.create_repository_dependency(repository=emboss_repository,
                                          filepath=dependency_path,
                                          repository_tuples=[repository_tuple],
                                          strings_displayed=strings_displayed,
                                          complex=False)

[docs]    def test_0040_generate_repository_dependency_with_invalid_changeset_revision(self):
        '''Generate a repository dependency for emboss 5 with an invalid changeset revision.'''
        dependency_path = self.generate_temp_path('test_0110', additional_paths=['simple', 'invalid'])
        repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
        url = self.url
        name = repository.name
        owner = repository.user.username
        changeset_revision = '!?invalid?!'
        strings_displayed = ['because the changeset revision is invalid.']
        repository_tuple = (url, name, owner, changeset_revision)
        self.create_repository_dependency(repository=emboss_repository,
                                          filepath=dependency_path,
                                          repository_tuples=[repository_tuple],
                                          strings_displayed=strings_displayed,
                                          complex=False)