Source code for tool_shed.test.functional.test_0470_tool_dependency_repository_type

import logging

from ..base.twilltestcase import (
    common,
    ShedTwillTestCase,
)

log = logging.getLogger(__name__)

category_name = "Test 0470 Tool dependency repository type"
category_description = "Test script 0470 for changing repository types."
package_libx11_repository_name = "package_x11_client_1_5_proto_7_0_0470"
package_libx11_repository_description = (
    "Contains a tool dependency definition that provides the X11 client libraries and core protocol header files."
)
package_libx11_repository_long_description = (
    "Xlib is an X Window System protocol client library written in the C programming language."
)
package_emboss_repository_name = "package_emboss_5_0_0_0470"
package_emboss_repository_description = (
    "Contains a tool dependency definition that downloads and compiles version 5.0.0 of the EMBOSS tool suite."
)
package_emboss_repository_long_description = 'EMBOSS is "The European Molecular Biology Open Software Suite".'
datatypes_repository_name = "emboss_datatypes_0470"
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = (
    "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
)
emboss_repository_name = "emboss_5_0470"
emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"

"""
1. Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml.
   Keep the repository type as the default "Unrestricted".

2. Create a repository named package_emboss_5_0_0 of type "Unrestricted" that has a repository dependency definition that defines the
   above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencies.xml file such that it does not have a changeset_revision
   defined so it will get automatically populated.

3. Create a repository named emboss_5 of type "Unrestricted" that has a tool-dependencies.xml file defining a complex repository dependency
   on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined
   so it will get automatically populated.

4. Add a comment to the tool_dependencies.xml file to be uploaded to the package_x11_client_1_5_prot_7_0 repository, creating a new installable
   changeset revision at the repository tip.

5. Add a comment to the tool_dependencies.xml file for the package_emboss_5_0_0 repository, eliminating the change set_revision attribute so
   that it gets automatically populated when uploaded. After uploading the file, the package_emboss_5_0_0 repository should have 2
   installable changeset revisions.

6. Add a comment to the tool_dependencies.xml file in the emboss_5 repository, eliminating the changeset_revision attribute so that it gets
   automatically populated when uploaded. After uploading the file, the emboss5 repository should have 2 installable metadata revisions.

7. Change the repository type of the package_x11_client_1_5_proto_7_0 repository to be tool_dependency_definition.

8. Change the repository type of the package_emboss_5_0_0 repository to be tool_dependency_definition.

9. Reset metadata on the package_emboss_5_0_0 repository. It should now have only its tip as the installable revision.

10. Reset metadata on the emboss_5 repository. It should now have only its tip as the installable revision.
"""


[docs]class TestEnvironmentInheritance(ShedTwillTestCase): """Test referencing environment variables that were defined in a separate tool dependency."""
[docs] def test_0000_initiate_users_and_category(self): """Create necessary user accounts and login as an admin user.""" 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) self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_2_email, username=common.test_user_2_name) test_user_2 = self.test_db_util.get_user(common.test_user_2_email) assert ( test_user_2 is not None ), f"Problem retrieving user with email {common.test_user_2_email} from the database" self.test_db_util.get_private_role(test_user_2) 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)
[docs] def test_0005_create_libx11_repository(self): """Create and populate package_x11_client_1_5_proto_7_0_0470. This is step 1 - Create and populate a repository named package_x11_client_1_5_proto_7_0. Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml. Keep the repository type as the default "Unrestricted". """ category = self.test_db_util.get_category_by_name(category_name) repository = self.get_or_create_repository( name=package_libx11_repository_name, description=package_libx11_repository_description, long_description=package_libx11_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[], ) # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository. self.upload_file( repository, filename="emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0010_create_emboss_5_0_0_repository(self): """Create and populate package_emboss_5_0_0_0470. This is step 2 - Create a repository named package_emboss_5_0_0 of type "Unrestricted". Create a repository named package_emboss_5_0_0 of type "Unrestricted" that has a repository dependency definition that defines the above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencues.xml file such that it does not have a changeset_revision defined so it will get automatically populated. """ category = self.test_db_util.get_category_by_name(category_name) repository = self.get_or_create_repository( name=package_emboss_repository_name, description=package_emboss_repository_description, long_description=package_emboss_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[], ) # Upload the edited tool dependency definition to the package_emboss_5_0_0 repository. self.upload_file( repository, filename="emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Populate package_emboss_5_0_0_0470 with tool dependency definitions.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0015_create_emboss_5_repository(self): """Create and populate emboss_5_0470. This is step 3 - Create a repository named emboss_5 of type "Unrestricted". Create a repository named emboss_5 of type "Unrestricted" that has a tool-dependencies.xml file defining a complex repository dependency on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined so it will get automatically populated. """ category = self.test_db_util.get_category_by_name(category_name) 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=[], ) # Populate emboss_5 with tool and dependency definitions. self.upload_file( repository, filename="emboss/0470_files/emboss_complex_dependency.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Populate emboss_5 with tool and dependency definitions.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0020_upload_updated_tool_dependency_to_package_x11(self): """Upload a new tool_dependencies.xml to package_x11_client_1_5_proto_7_0_0470. This is step 4 - Add a comment to the tool_dependencies.xml file to be uploaded to the package_x11_client_1_5_prot_7_0 repository, creating a new installable changeset revision at the repository tip. """ package_x11_repository = self.test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name ) # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository. self.upload_file( package_x11_repository, filename="emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.", strings_displayed=[], strings_not_displayed=[], ) assert len(package_x11_repository.metadata_revisions) == 1, ( "package_x11_client_1_5_proto_7_0_0470 has incorrect number of metadata revisions, expected 1 but found %d" % len(package_x11_repository.metadata_revisions) )
[docs] def test_0025_upload_updated_tool_dependency_to_package_emboss(self): """Upload a new tool_dependencies.xml to package_emboss_5_0_0_0470. This is step 5 - Add a comment to the tool_dependencies.xml file for the package_emboss_5_0_0 repository, eliminating the change set_revision attribute so that it gets automatically populated when uploaded. After uploading the file, the package_emboss_5_0_0 repository should have 2 installable changeset revisions. """ package_emboss_repository = self.test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name ) # Populate package_emboss_5_0_0_0470 with updated tool dependency definition. self.upload_file( package_emboss_repository, filename="emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Populate package_emboss_5_0_0_0470 with tool dependency definitions.", strings_displayed=[], strings_not_displayed=[], ) assert ( len(package_emboss_repository.metadata_revisions) == 2 ), "package_emboss_5_0_0_0470 has incorrect number of metadata revisions, expected 2 but found %d" % len( package_emboss_repository.metadata_revisions )
[docs] def test_0030_upload_updated_tool_dependency_to_emboss_5_repository(self): """Upload a new tool_dependencies.xml to emboss_5_0470. This is step 6 - Add a comment to the tool_dependencies.xml file in the emboss_5 repository, eliminating the changeset_revision attribute so that it gets automatically populated when uploaded. After uploading the file, the emboss5 repository should have 2 installable metadata revisions. """ emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) # Populate package_emboss_5_0_0_0470 with updated tool dependency definition. self.upload_file( emboss_repository, filename="emboss/0470_files/tool_dependencies.xml", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Upload updated complex repository dependency definition to emboss_5_0470.", strings_displayed=[], strings_not_displayed=[], ) assert ( len(emboss_repository.metadata_revisions) == 2 ), "package_emboss_5_0_0_0470 has incorrect number of metadata revisions"
[docs] def test_0035_modify_package_x11_repository_type(self): """Set package_x11_client_1_5_proto_7_0 type tool_dependency_definition. This is step 7 - Change the repository type of the package_x11_client_1_5_proto_7_0 repository to be tool_dependency_definition. """ package_x11_repository = self.test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name ) self.edit_repository_information(package_x11_repository, repository_type="tool_dependency_definition")
[docs] def test_0040_modify_package_emboss_repository_type(self): """Set package_emboss_5_0_0 to type tool_dependency_definition. This is step 8 - Change the repository type of the package_emboss_5_0_0 repository to be tool_dependency_definition. """ package_emboss_repository = self.test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name ) self.edit_repository_information(package_emboss_repository, repository_type="tool_dependency_definition")
[docs] def test_0045_reset_repository_metadata(self): """Reset metadata on package_emboss_5_0_0_0470 and package_x11_client_1_5_proto_7_0. This is step 9 - Reset metadata on the package_emboss_5_0_0 and package_x11_client_1_5_proto_7_0 repositories. They should now have only their tip as the installable revision. """ package_emboss_repository = self.test_db_util.get_repository_by_name_and_owner( package_emboss_repository_name, common.test_user_1_name ) package_x11_repository = self.test_db_util.get_repository_by_name_and_owner( package_libx11_repository_name, common.test_user_1_name ) self.reset_repository_metadata(package_emboss_repository) self.reset_repository_metadata(package_x11_repository) assert ( len(package_emboss_repository.metadata_revisions) == 1 ), "Repository package_emboss_5_0_0 has %d installable revisions, expected 1." % len( package_emboss_repository.metadata_revisions ) assert ( len(package_x11_repository.metadata_revisions) == 1 ), "Repository package_x11_client_1_5_proto_7_0 has %d installable revisions, expected 1." % len( package_x11_repository.metadata_revisions )
[docs] def test_0050_reset_emboss_5_metadata(self): """Reset metadata on emboss_5. This is step 10 - Reset metadata on the emboss_5 repository. It should now have only its tip as the installable revision. """ emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) self.reset_repository_metadata(emboss_repository) assert ( len(emboss_repository.metadata_revisions) == 1 ), "Repository emboss_5 has %d installable revisions, expected 1." % len(emboss_repository.metadata_revisions)