Source code for tool_shed.test.functional.test_1170_prior_installation_required

import logging

from ..base.twilltestcase import common, ShedTwillTestCase

log = logging.getLogger(__name__)

column_repository_name = 'column_maker_0150'
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"

convert_repository_name = 'convert_chars_0150'
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"

category_name = 'Test 0150 Simple Prior Installation'
category_description = 'Test 0150 Simple Prior Installation'

'''
Create column_maker and convert_chars.

Column maker repository dependency:
<repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />

Verify display.

Galaxy side:

Install column_maker.
Verify that convert_chars was installed first, contrary to the ordering that would be present without prior_installation_required.
'''

running_standalone = False


[docs]class TestSimplePriorInstallation(ShedTwillTestCase):
    '''Test features related to datatype converters.'''

[docs]    def test_0000_initiate_users(self):
        """Create necessary user accounts."""
        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)
        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_convert_repository(self):
        '''Create and populate convert_chars_0150.'''
        global running_standalone
        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=convert_repository_name,
                                                   description=convert_repository_description,
                                                   long_description=convert_repository_long_description,
                                                   owner=common.test_user_1_name,
                                                   category_id=self.security.encode_id(category.id),
                                                   strings_displayed=[])
        if self.repository_is_new(repository):
            running_standalone = True
            self.upload_file(repository,
                             filename='convert_chars/convert_chars.tar',
                             filepath=None,
                             valid_tools_only=True,
                             uncompress_file=True,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded convert_chars tarball.',
                             strings_displayed=[],
                             strings_not_displayed=[])

[docs]    def test_0010_create_column_repository(self):
        '''Create and populate convert_chars_0150.'''
        global running_standalone
        category = self.create_category(name=category_name, description=category_description)
        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=[])
        if running_standalone:
            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='Uploaded column_maker tarball.',
                             strings_displayed=[],
                             strings_not_displayed=[])

[docs]    def test_0015_create_repository_dependency(self):
        '''Create a repository dependency specifying convert_chars.'''
        '''
        Column maker repository dependency:
            <repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="<tip>" prior_installation_required="True" />
        '''
        global running_standalone
        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
        if running_standalone:
            dependency_xml_path = self.generate_temp_path('test_1150', additional_paths=['column'])
            convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
            self.create_repository_dependency(repository=column_repository,
                                              repository_tuples=[convert_tuple],
                                              filepath=dependency_xml_path,
                                              prior_installation_required=True)

[docs]    def test_0020_verify_repository_dependency(self):
        '''Verify that the previously generated repositiory dependency displays correctly.'''
        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
        self.check_repository_dependency(repository=column_repository,
                                         depends_on_repository=convert_repository,
                                         depends_on_changeset_revision=None,
                                         changeset_revision=None)

[docs]    def test_0025_install_column_repository(self):
        '''Install column_maker_0150.'''
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
        preview_strings_displayed = ['column_maker_0150', self.get_repository_tip(column_repository)]
        strings_displayed = ['Choose the tool panel section']
        self.install_repository(column_repository_name,
                                common.test_user_1_name,
                                category_name,
                                install_tool_dependencies=False,
                                install_repository_dependencies=True,
                                preview_strings_displayed=preview_strings_displayed,
                                strings_displayed=strings_displayed,
                                strings_not_displayed=[],
                                post_submit_strings_displayed=['column_maker_0150', 'New'],
                                includes_tools_for_display_in_tool_panel=True)

[docs]    def test_0030_verify_installation_order(self):
        '''Verify that convert_chars_0150 was installed before column_maker_0150.'''
        column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name)
        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(convert_repository_name, common.test_user_1_name)
        # Column maker was selected for installation, so convert chars should have been installed first, as reflected by the update_time field.
        assert column_repository.update_time > convert_repository.update_time, 'Error: column_maker_0150 shows an earlier update time than convert_chars_0150'