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Source code for tool_shed.test.functional.test_0540_get_all_metadata_from_api

import logging

from ..base.twilltestcase import common, ShedTwillTestCase

log = logging.getLogger(__name__)

repositories = dict(column=dict(name='column_maker_0540',
                                description='Description for column_maker_0540',
                                long_description='Long description for column_maker_0540'),
                    convert=dict(name='convert_chars_0540',
                                 description='Description for convert_chars_0540',
                                 long_description='Long description for convert_chars_0540'),
                    bwa=dict(name='package_bwa_0_5_9_0540',
                             description='Description for package_bwa_0_5_9_0540',
                             long_description='Long description for package_bwa_0_5_9_0540'))

category_name = 'Test 0540'
category_description = 'Verify API endpoint to retrieve all metadata'

'''
1. Create repository column_maker_0540 as user user1.

2. Create repository convert_chars_0540 with dependency on column_maker_0540.

3. Create repository package_bwa_0_5_9_0540.

4. Create dependency on package_bwa_0_5_9_0540 for convert_chars_0540.

5. Load /api/repositories/convert_chars_0540.id/metadata and verify contents.
'''


[docs]class TestGetAllMetadata(ShedTwillTestCase): '''Verify that the code correctly handles the repository admin role.'''
[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_0540.''' 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=repositories['bwa']['name'], description=repositories['bwa']['description'], long_description=repositories['bwa']['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['bwa']['name'] self.upload_file(repository, filename='0540_files/package_bwa/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_convert_repository(self): '''Create the convert_chars_0540 repository.''' category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository(name=repositories['convert']['name'], description=repositories['convert']['description'], long_description=repositories['convert']['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['convert']['name'] self.upload_file(repository, filename='0540_files/convert_chars/convert_chars.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded column maker 1.0.', strings_displayed=[], strings_not_displayed=[]) # Add a dependency on BWA. self.upload_file(repository, filename='0540_files/convert_chars/tool_dependencies.xml', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded column maker 1.0.', strings_displayed=[], strings_not_displayed=[]) # Visit the manage repository page for convert_chars_0540. self.display_manage_repository_page(repository, strings_displayed=[repositories['bwa']['name']])
[docs] def test_0015_create_column_repository(self): '''Create the column_maker_0540 repository.''' category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository(name=repositories['column']['name'], description=repositories['column']['description'], long_description=repositories['column']['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['column']['name'] self.upload_file(repository, filename='0540_files/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 1.0.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0020_create_repository_dependency(self): '''Make column_maker depend on convert_chars.''' repository = self.test_db_util.get_repository_by_name_and_owner(repositories['column']['name'], common.test_user_1_name) self.upload_file(repository, filename='0540_files/column_maker/repository_dependencies.xml', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded column maker 2.0.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0025_verify_dependency_json(self): ''' Load the API endpoint to retrieve all repository metadata and verify that all three repository names are displayed. ''' repository = self.test_db_util.get_repository_by_name_and_owner(repositories['column']['name'], common.test_user_1_name) strings_displayed = [repositories['column']['name'], repositories['convert']['name'], repositories['bwa']['name']] self.fetch_repository_metadata(repository, strings_displayed=strings_displayed, strings_not_displayed=None)