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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, 'Problem retrieving user with email %s from the database' % common.admin_email
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, 'Problem retrieving user with email %s from the database' % common.test_user_2_email
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, 'Problem retrieving user with email %s from the database' % common.test_user_1_email
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)