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Source code for tool_shed.test.functional.test_0100_complex_repository_dependencies

import logging
import os

from ..base.twilltestcase import common, ShedTwillTestCase

log = logging.getLogger(__name__)

bwa_base_repository_name = 'bwa_base_repository_0100'
bwa_base_repository_description = "BWA Base"
bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"

bwa_package_repository_name = 'package_bwa_0_5_9_0100'
bwa_package_repository_description = "BWA Tool"
bwa_package_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9."

category_name = 'Test 0100 Complex Repository Dependencies'
category_description = 'Test 0100 Complex Repository Dependencies'


[docs]class TestComplexRepositoryDependencies(ShedTwillTestCase): '''Test features related to complex repository dependencies.'''
[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, 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_bwa_package_repository(self): '''Create and populate package_bwa_0_5_9_0100.''' category = self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) # Create a repository named package_bwa_0_5_9_0100 owned by user1. repository = self.get_or_create_repository(name=bwa_package_repository_name, description=bwa_package_repository_description, long_description=bwa_package_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[]) self.upload_file(repository, filename='bwa/complex/tool_dependencies.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool_dependencies.xml.', strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'], strings_not_displayed=[]) # Visit the manage repository page for package_bwa_0_5_9_0100. self.display_manage_repository_page(repository, strings_displayed=['Tool dependencies', 'will not be', 'to this repository'])
[docs] def test_0010_create_bwa_base_repository(self): '''Create and populate bwa_base_0100.''' category = self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) # Create a repository named bwa_base_repository_0100 owned by user1. repository = self.get_or_create_repository(name=bwa_base_repository_name, description=bwa_base_repository_description, long_description=bwa_base_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[]) # Populate the repository named bwa_base_repository_0100 with a bwa_base tool archive. self.upload_file(repository, filename='bwa/complex/bwa_base.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0015_generate_complex_repository_dependency_invalid_shed_url(self): '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.''' dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'invalid']) # The repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name) url = 'http://http://this is not an url!' name = 'package_bwa_0_5_9_0100' owner = 'user1' changeset_revision = self.get_repository_tip(tool_repository) strings_displayed = ['Repository dependencies are currently supported only within the same tool shed'] # Populate the dependent repository named bwa_base_repository_0100 with an invalid tool_dependencies.xml file. repository_tuple = (url, name, owner, changeset_revision) self.create_repository_dependency(repository=base_repository, filepath=dependency_path, repository_tuples=[repository_tuple], strings_displayed=strings_displayed, complex=True, package='bwa', version='0.5.9')
[docs] def test_0020_generate_complex_repository_dependency_invalid_repository_name(self): '''Generate and upload a complex repository definition that specifies an invalid repository name.''' dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'invalid']) # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name) url = self.url name = 'invalid_repository!?' owner = 'user1' changeset_revision = self.get_repository_tip(tool_repository) strings_displayed = ['because the name is invalid'] # Populate the dependent base_repository named package_bwa_0_5_9_0100 with an invalid tool_dependencies.xml file. repository_tuple = (url, name, owner, changeset_revision) self.create_repository_dependency(repository=base_repository, filepath=dependency_path, repository_tuples=[repository_tuple], strings_displayed=strings_displayed, complex=True, package='bwa', version='0.5.9')
[docs] def test_0025_generate_complex_repository_dependency_invalid_owner_name(self): '''Generate and upload a complex repository definition that specifies an invalid owner.''' dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'invalid']) # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name) url = self.url name = 'package_bwa_0_5_9_0100' owner = 'invalid_owner!?' changeset_revision = self.get_repository_tip(tool_repository) strings_displayed = ['because the owner is invalid.'] repository_tuple = (url, name, owner, changeset_revision) self.create_repository_dependency(repository=base_repository, filepath=dependency_path, repository_tuples=[repository_tuple], strings_displayed=strings_displayed, complex=True, package='bwa', version='0.5.9')
[docs] def test_0030_generate_complex_repository_dependency_invalid_changeset_revision(self): '''Generate and upload a complex repository definition that specifies an invalid changeset revision.''' dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'invalid']) # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name) # The repository named package_bwa_0_5_9_0100 is the required repository. url = self.url name = 'package_bwa_0_5_9_0100' owner = 'user1' changeset_revision = '1234abcd' strings_displayed = ['because the changeset revision is invalid.'] repository_tuple = (url, name, owner, changeset_revision) self.create_repository_dependency(repository=base_repository, filepath=dependency_path, repository_tuples=[repository_tuple], strings_displayed=strings_displayed, complex=True, package='bwa', version='0.5.9')
[docs] def test_0035_generate_complex_repository_dependency(self): '''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.''' # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name) dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex']) url = self.url name = 'package_bwa_0_5_9_0100' owner = 'user1' changeset_revision = self.get_repository_tip(tool_repository) repository_tuple = (url, name, owner, changeset_revision) self.create_repository_dependency(repository=base_repository, filepath=dependency_path, repository_tuples=[repository_tuple], complex=True, package='bwa', version='0.5.9') self.check_repository_dependency(base_repository, depends_on_repository=tool_repository) self.display_manage_repository_page(base_repository, strings_displayed=['bwa', '0.5.9', 'package', changeset_revision])
[docs] def test_0040_generate_tool_dependency(self): '''Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.''' # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name) # The repository named package_bwa_0_5_9_0100 is the required repository. tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name) previous_changeset = self.get_repository_tip(tool_repository) old_tool_dependency = self.get_filename(os.path.join('bwa', 'complex', 'readme', 'tool_dependencies.xml')) new_tool_dependency_path = self.generate_temp_path('test_1100', additional_paths=['tool_dependency']) xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, 'tool_dependencies.xml')) # Generate a tool_dependencies.xml file that points to an arbitrary file in the local filesystem. open(xml_filename, 'w').write(open(old_tool_dependency) .read().replace('__PATH__', self.get_filename('bwa/complex'))) self.upload_file(tool_repository, filename=xml_filename, filepath=new_tool_dependency_path, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded new tool_dependencies.xml.', strings_displayed=[], strings_not_displayed=[]) # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. repository_tip = self.get_repository_tip(tool_repository) strings_displayed = ['bwa', '0.5.9', 'package'] strings_displayed.append(repository_tip) strings_not_displayed = [previous_changeset] self.display_manage_repository_page(tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed) # Visit the manage page of the package_bwa_0_5_9_0100 to confirm the valid tool dependency definition. self.display_manage_repository_page(tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed) # Visit the manage page of the bwa_base_repository_0100 to confirm the valid tool dependency definition # and the updated changeset revision (updated tip) of the package_bwa_0_5_9_0100 repository is displayed # as the required repository revision. The original revision defined in the previously uploaded # tool_dependencies.xml file will be updated. self.display_manage_repository_page(base_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed)