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, '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_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, 'r')
                                 .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)