Source code for tool_shed.test.functional.test_0550_metadata_updated_dependencies

import logging

from ..base.twilltestcase import common, ShedTwillTestCase

log = logging.getLogger(__name__)

repositories = dict(freebayes=dict(name='package_freebayes_0550',
                                   description='Description for package_freebayes_0550',
                                   long_description='Long description for package_freebayes_0550'),
                    samtools=dict(name='package_samtools_0550',
                                  description='Description for package_samtools_0550',
                                  long_description='Long description for package_samtools_0550'),
                    filtering=dict(name='filtering_0550',
                                   description='Description for filtering_0550',
                                   long_description='Long description for filtering_0550'))

category_name = 'Test 0550'
category_description = 'Verify metadata updates'

'''
1. Create repository package_freebayes_0550.

2. Create repository package_samtools_0550.

3. Create repository filtering_0550.

4. Create dependency on package_freebayes_0550 for filtering_0550.

5. Create dependency on package_samtools_0550 for filtering_0550.

6. Update package_freebayes_0550 and package_samtools_0550.

5. Load /api/repositories/{filtering_0550}.id/metadata and verify contents.
'''


[docs]class TestGetUpdatedMetadata(ShedTwillTestCase):
    '''Verify that updated repositories still have correct dependency links.'''

[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_freebayes_repository(self):
        '''Create and populate package_freebayes_0550.'''
        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_freebayes_0550 owned by user1.
        freebayes = self.get_or_create_repository(name=repositories['freebayes']['name'],
                                                  description=repositories['freebayes']['description'],
                                                  long_description=repositories['freebayes']['long_description'],
                                                  owner=common.test_user_1_name,
                                                  category_id=self.security.encode_id(category.id),
                                                  strings_displayed=[])
        assert freebayes is not None, 'Error creating freebayes %s' % repositories['freebayes']['name']
        self.upload_file(freebayes,
                         filename='0550_files/package_freebayes_1_0550.tgz',
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=False,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded.',
                         strings_displayed=['has been successfully uploaded to the repository', 'contains a single file'],
                         strings_not_displayed=None)
        # Visit the manage repository page for package_freebayes_0_5_9_0100.
        self.display_manage_repository_page(freebayes, strings_displayed=['Tool dependencies', 'will not be', 'to this repository'])

[docs]    def test_0010_create_samtools_repository(self):
        '''Create and populate the package_samtools_0550 repository.'''
        category = self.create_category(name=category_name, description=category_description)
        samtools = self.get_or_create_repository(name=repositories['samtools']['name'],
                                                 description=repositories['samtools']['description'],
                                                 long_description=repositories['samtools']['long_description'],
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id(category.id),
                                                 strings_displayed=[])
        assert samtools is not None, 'Error creating samtools %s' % repositories['samtools']['name']
        self.upload_file(samtools,
                         filename='0550_files/package_samtools_1_0550.tgz',
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded samtools 1.0.',
                         strings_displayed=['has been successfully uncompressed and uploaded to the repository'],
                         strings_not_displayed=[])

[docs]    def test_0015_create_filtering_repository(self):
        '''Create the filtering_0550 repository.'''
        category = self.create_category(name=category_name, description=category_description)
        repository = self.get_or_create_repository(name=repositories['filtering']['name'],
                                                   description=repositories['filtering']['description'],
                                                   long_description=repositories['filtering']['long_description'],
                                                   owner=common.test_user_1_name,
                                                   category_id=self.security.encode_id(category.id),
                                                   strings_displayed=[])
        assert repository is not None, 'Error creating repository %s' % repositories['filtering']['name']
        self.upload_file(repository,
                         filename='0550_files/filtering_1.0.tgz',
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded filtering 1.0.',
                         strings_displayed=['has been successfully uncompressed and uploaded to the repository'],
                         strings_not_displayed=[])

[docs]    def test_0020_check_repository_dependency(self):
        '''Make filtering depend on samtools and freebayes.'''
        freebayes = self.test_db_util.get_repository_by_name_and_owner(repositories['freebayes']['name'],
                                                                     common.test_user_1_name)
        samtools = self.test_db_util.get_repository_by_name_and_owner(repositories['samtools']['name'],
                                                                      common.test_user_1_name)
        filtering = self.test_db_util.get_repository_by_name_and_owner(repositories['filtering']['name'],
                                                                       common.test_user_1_name)
        strings_displayed = [self.security.encode_id(freebayes.id), self.security.encode_id(samtools.id)]
        self.display_manage_repository_page(filtering, strings_displayed=strings_displayed)

[docs]    def test_0025_update_dependent_repositories(self):
        '''
        Update freebayes and samtools, load the API endpoint again.
        '''
        freebayes = self.test_db_util.get_repository_by_name_and_owner(repositories['freebayes']['name'],
                                                                     common.test_user_1_name)
        samtools = self.test_db_util.get_repository_by_name_and_owner(repositories['samtools']['name'],
                                                                      common.test_user_1_name)
        filtering = self.test_db_util.get_repository_by_name_and_owner(repositories['filtering']['name'],
                                                                       common.test_user_1_name)
        self.upload_file(freebayes,
                         filename='0550_files/package_freebayes_2_0550.tgz',
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded freebayes 2.0.',
                         strings_displayed=['has been successfully uncompressed and uploaded to the repository'],
                         strings_not_displayed=[])
        self.upload_file(samtools,
                         filename='0550_files/package_samtools_2_0550.tgz',
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded samtools 2.0.',
                         strings_displayed=['has been successfully uncompressed and uploaded to the repository'],
                         strings_not_displayed=[])
        strings_displayed = [repositories['freebayes']['name'],
                             repositories['samtools']['name'],
                             repositories['filtering']['name']]
        self.fetch_repository_metadata(filtering, strings_displayed=strings_displayed, strings_not_displayed=None)