Source code for tool_shed.test.functional.test_0070_invalid_tool

from ..base.twilltestcase import common, ShedTwillTestCase

repository_name = 'bismark_0070'
repository_description = "Galaxy's bismark wrapper"
repository_long_description = "Long description of Galaxy's bismark wrapper"
category_name = 'Test 0070 Invalid Tool Revisions'
category_description = 'Tests for a repository with invalid tool revisions.'


[docs]class TestBismarkRepository(ShedTwillTestCase):
    '''Testing bismark with valid and invalid tool entries.'''

[docs]    def test_0000_create_or_login_admin_user(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, f'Problem retrieving user with email {common.test_user_1_email} from the database'
        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, f'Problem retrieving user with email {common.admin_email} from the database'
        self.test_db_util.get_private_role(admin_user)

[docs]    def test_0005_create_category_and_repository(self):
        """Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool."""
        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=repository_name,
                                                   description=repository_description,
                                                   long_description=repository_long_description,
                                                   owner=common.test_user_1_name,
                                                   category_id=self.security.encode_id(category.id),
                                                   strings_displayed=[])
        self.upload_file(repository,
                         filename='bismark/bismark.tar',
                         filepath=None,
                         valid_tools_only=False,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded bismark tarball.',
                         strings_displayed=[],
                         strings_not_displayed=[])
        self.display_manage_repository_page(repository, strings_displayed=['Invalid tools'])
        invalid_revision = self.get_repository_tip(repository)
        self.upload_file(repository,
                         filename='bismark/bismark_methylation_extractor.xml',
                         filepath=None,
                         valid_tools_only=False,
                         uncompress_file=False,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded an updated tool xml.',
                         strings_displayed=[],
                         strings_not_displayed=[])
        valid_revision = self.get_repository_tip(repository)
        self.test_db_util.refresh(repository)
        tool_guid = f"{self.url.replace('http://', '').rstrip('/')}/repos/user1/bismark_0070/bismark_methylation_extractor/0.7.7.3"
        tool_metadata_strings_displayed = [tool_guid,
                                           '0.7.7.3',  # The tool version.
                                           'bismark_methylation_extractor',  # The tool ID.
                                           'Bismark',  # The tool name.
                                           'methylation extractor']  # The tool description.
        tool_page_strings_displayed = ['Bismark (version 0.7.7.3)']
        self.check_repository_tools_for_changeset_revision(repository,
                                                           valid_revision,
                                                           tool_metadata_strings_displayed=tool_metadata_strings_displayed,
                                                           tool_page_strings_displayed=tool_page_strings_displayed)
        self.check_repository_invalid_tools_for_changeset_revision(repository, invalid_revision)