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Source code for tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions
from ..base.twilltestcase import (
common,
ShedTwillTestCase,
)
datatypes_repository_name = "emboss_datatypes_0030"
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_0030"
emboss_5_repository_name = "emboss_5_0030"
emboss_6_repository_name = "emboss_6_0030"
emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030"
emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030"
base_datatypes_count = 0
repository_datatypes_count = 0
running_standalone = False
[docs]class RepositoryWithDependencyRevisions(ShedTwillTestCase):
"""Test installing a repository with dependency revisions."""
[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
), f"Problem retrieving user with email {common.test_user_1_email} from the database"
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, f"Problem retrieving user with email {common.admin_email} from the database"
self.test_db_util.get_private_role(admin_user)
self.galaxy_login(email=common.admin_email, username=common.admin_username)
galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
assert (
galaxy_admin_user is not None
), f"Problem retrieving user with email {common.admin_email} from the database"
self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
[docs] def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0030 category and add repositories to it, if necessary."""
global repository_datatypes_count
global running_standalone
category = self.create_category(
name="Test 0030 Repository Dependency Revisions", description="Test 0030 Repository Dependency Revisions"
)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
datatypes_repository = self.get_or_create_repository(
name=datatypes_repository_name,
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[],
)
if self.repository_is_new(datatypes_repository):
running_standalone = True
self.upload_file(
datatypes_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=[],
)
emboss_5_repository = self.get_or_create_repository(
name=emboss_5_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(
emboss_5_repository,
filename="emboss/emboss.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded tool tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"])
datatypes_tuple = (
self.url,
datatypes_repository.name,
datatypes_repository.user.username,
self.get_repository_tip(datatypes_repository),
)
self.create_repository_dependency(
repository=emboss_5_repository,
repository_tuples=[datatypes_tuple],
filepath=repository_dependencies_path,
)
emboss_6_repository = self.get_or_create_repository(
name=emboss_6_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(
emboss_6_repository,
filename="emboss/emboss.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded tool tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "6"])
datatypes_tuple = (
self.url,
datatypes_repository.name,
datatypes_repository.user.username,
self.get_repository_tip(datatypes_repository),
)
self.create_repository_dependency(
repository=emboss_6_repository,
repository_tuples=[datatypes_tuple],
filepath=repository_dependencies_path,
)
emboss_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(
emboss_repository,
filename="emboss/emboss.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded tool tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"])
dependency_tuple = (
self.url,
emboss_5_repository.name,
emboss_5_repository.user.username,
self.get_repository_tip(emboss_5_repository),
)
self.create_repository_dependency(
repository=emboss_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path,
)
dependency_tuple = (
self.url,
emboss_6_repository.name,
emboss_6_repository.user.username,
self.get_repository_tip(emboss_6_repository),
)
self.create_repository_dependency(
repository=emboss_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path,
)
repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))
[docs] def test_0010_browse_tool_shed(self):
"""Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
self.browse_tool_shed(url=self.url, strings_displayed=["Test 0030 Repository Dependency Revisions"])
category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
self.browse_category(category, strings_displayed=["emboss_0030"])
self.preview_repository_in_tool_shed(
"emboss_0030", common.test_user_1_name, strings_displayed=["emboss_0030", "Valid tools"]
)
[docs] def test_0015_install_emboss_repository(self):
"""Install the emboss repository without installing tool dependencies."""
global repository_datatypes_count
global base_datatypes_count
global running_standalone
base_datatypes_count = int(self.get_datatypes_count())
strings_displayed = ["Handle", "Never installed", "tool dependencies", "emboss", "5.0.0", "package"]
self.install_repository(
"emboss_0030",
common.test_user_1_name,
"Test 0030 Repository Dependency Revisions",
strings_displayed=strings_displayed,
install_tool_dependencies=False,
new_tool_panel_section_label="test_1030",
)
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
"emboss_0030", common.test_user_1_name
)
strings_displayed = [
"emboss_0030",
"Galaxy wrappers for Emboss version 5.0.0 tools for test 0030",
"user1",
self.url.replace("http://", ""),
installed_repository.installed_changeset_revision,
]
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
strings_displayed.extend(["Installed tool shed repository", "Valid tools", "antigenic"])
self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
self.verify_tool_metadata_for_installed_repository(installed_repository)
self.update_installed_repository(installed_repository, strings_displayed=["there are no updates available"])
current_datatypes = int(self.get_datatypes_count())
if running_standalone:
assert (
current_datatypes == base_datatypes_count + repository_datatypes_count
), "Installing emboss did not add new datatypes."
else:
assert current_datatypes == base_datatypes_count, "Installing emboss added new datatypes."
[docs] def test_0025_verify_installed_repository_metadata(self):
"""Verify that resetting the metadata on an installed repository does not change the metadata."""
self.verify_installed_repository_metadata_unchanged("emboss_0030", common.test_user_1_name)