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Source code for tool_shed.test.functional.test_0090_tool_search

from ..base.twilltestcase import common, ShedTwillTestCase

emboss_datatypes_repository_name = 'emboss_datatypes_0090'
emboss_datatypes_repository_description = "Datatypes for emboss"
emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes"

emboss_repository_name = 'emboss_0090'
emboss_repository_description = "Galaxy's emboss tool"
emboss_repository_long_description = "Long description of Galaxy's emboss tool"

filtering_repository_name = 'filtering_0090'
filtering_repository_description = "Galaxy's filtering tool"
filtering_repository_long_description = "Long description of Galaxy's filtering tool"

freebayes_repository_name = 'freebayes_0090'
freebayes_repository_description = "Galaxy's freebayes tool"
freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"

bwa_base_repository_name = 'bwa_base_0090'
bwa_base_repository_description = "BWA Base"
bwa_base_repository_long_description = "NT space mapping with BWA"

bwa_color_repository_name = 'bwa_color_0090'
bwa_color_repository_description = "BWA Color"
bwa_color_repository_long_description = "Color space mapping with BWA"

category_name = 'Test 0090 Tool Search And Installation'
category_description = 'Test 0090 Tool Search And Installation'


[docs]class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase): '''Test more features related to 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_base_repository(self): '''Create and populate bwa_base_0090.''' 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=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=[]) self.upload_file(repository, filename='bwa/bwa_base.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded BWA tarball.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0010_create_bwa_color_repository(self): '''Create and populate bwa_color_0090.''' 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=bwa_color_repository_name, description=bwa_color_repository_description, long_description=bwa_color_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/bwa_color.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded BWA color tarball.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0015_create_emboss_datatypes_repository(self): '''Create and populate emboss_datatypes_0090.''' 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=emboss_datatypes_repository_name, description=emboss_datatypes_repository_description, long_description=emboss_datatypes_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[]) self.upload_file(repository, filename='emboss/datatypes/datatypes_conf.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded datatypes_conf.xml.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0020_create_emboss_repository(self): '''Create and populate emboss_0090.''' category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository(name=emboss_repository_name, description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[]) self.upload_file(repository, filename='emboss/emboss.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded emboss tarball.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0025_create_filtering_repository(self): '''Create and populate filtering_0090.''' category = self.create_category(name=category_name, description=category_description) filtering_repository = self.get_or_create_repository(name=filtering_repository_name, description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[]) self.upload_file(filtering_repository, filename='filtering/filtering_1.1.0.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded filtering 1.1.0 tarball.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0030_create_freebayes_repository(self): '''Create and populate freebayes_0090.''' category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository(name=freebayes_repository_name, description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[]) self.upload_file(repository, filename='freebayes/freebayes.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded freebayes tarball.', strings_displayed=[], strings_not_displayed=[])
[docs] def test_0035_create_and_upload_dependency_definitions(self): '''Create and upload repository dependency definitions.''' bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_color_repository_name, common.test_user_1_name) bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name) emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name) freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name) dependency_xml_path = self.generate_temp_path('test_0090', additional_paths=['freebayes']) freebayes_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository)) emboss_tuple = (self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip(emboss_repository)) datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository)) filtering_tuple = (self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip(filtering_repository)) self.create_repository_dependency(repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path) self.create_repository_dependency(repository=filtering_repository, repository_tuples=[freebayes_tuple], filepath=dependency_xml_path) self.create_repository_dependency(repository=bwa_base_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path) self.create_repository_dependency(repository=bwa_color_repository, repository_tuples=[filtering_tuple], filepath=dependency_xml_path)
[docs] def test_0040_verify_repository_dependencies(self): '''Verify the generated dependency structure.''' bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_color_repository_name, common.test_user_1_name) bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name) emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name) emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name) freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name) self.check_repository_dependency(emboss_repository, emboss_datatypes_repository) self.check_repository_dependency(filtering_repository, freebayes_repository) self.check_repository_dependency(bwa_base_repository, emboss_repository) self.check_repository_dependency(bwa_color_repository, filtering_repository)