import logging
import os
from ..base import common
from ..base.api import skip_if_api_v2
from ..base.twilltestcase import ShedTwillTestCase
log = logging.getLogger(__name__)
bwa_base_repository_name = "bwa_base_repository_0100"
bwa_base_repository_description = "BWA Base"
bwa_base_repository_long_description = (
"BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"
)
bwa_package_repository_name = "package_bwa_0_5_9_0100"
bwa_package_repository_description = "BWA Tool"
bwa_package_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9."
category_name = "Test 0100 Complex Repository Dependencies"
category_description = "Test 0100 Complex Repository Dependencies"
[docs]
class TestComplexRepositoryDependencies(ShedTwillTestCase):
"""Test features related to complex 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)
self.login(email=common.admin_email, username=common.admin_username, explicit_logout=True)
[docs]
def test_0005_create_bwa_package_repository(self):
"""Create and populate package_bwa_0_5_9_0100."""
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=bwa_package_repository_name,
description=bwa_package_repository_description,
long_description=bwa_package_repository_long_description,
owner=common.test_user_1_name,
category=category,
strings_displayed=[],
)
self.add_file_to_repository(repository, "bwa/complex/tool_dependencies.xml")
if not self.is_v2:
# 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_bwa_base_repository(self):
"""Create and populate bwa_base_0100."""
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 bwa_base_repository_0100 owned by user1.
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=category,
strings_displayed=[],
)
# Populate the repository named bwa_base_repository_0100 with a bwa_base tool archive.
self.commit_tar_to_repository(
repository,
"bwa/complex/bwa_base.tar",
commit_message="Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.",
)
[docs]
def test_0015_generate_complex_repository_dependency_invalid_shed_url(self):
"""Generate and upload a complex repository definition that specifies an invalid tool shed URL."""
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "invalid"])
# The repository named bwa_base_repository_0100 is the dependent repository.
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
# The repository named package_bwa_0_5_9_0100 is the required repository.
tool_repository = self._get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
url = "http://http://this is not an url!"
name = "package_bwa_0_5_9_0100"
owner = "user1"
changeset_revision = self.get_repository_tip(tool_repository)
strings_displayed = ["Repository dependencies are currently supported only within the same tool shed"]
# Populate the dependent repository named bwa_base_repository_0100 with an invalid tool_dependencies.xml file.
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(
repository=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=True,
package="bwa",
version="0.5.9",
)
[docs]
def test_0020_generate_complex_repository_dependency_invalid_repository_name(self):
"""Generate and upload a complex repository definition that specifies an invalid repository name."""
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "invalid"])
# The base_repository named bwa_base_repository_0100 is the dependent repository.
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
# The repository named package_bwa_0_5_9_0100 is the required repository.
tool_repository = self._get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
url = self.url
name = "invalid_repository!?"
owner = "user1"
changeset_revision = self.get_repository_tip(tool_repository)
strings_displayed = ["because the name is invalid"]
# Populate the dependent base_repository named package_bwa_0_5_9_0100 with an invalid tool_dependencies.xml file.
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(
repository=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=True,
package="bwa",
version="0.5.9",
)
[docs]
def test_0025_generate_complex_repository_dependency_invalid_owner_name(self):
"""Generate and upload a complex repository definition that specifies an invalid owner."""
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "invalid"])
# The base_repository named bwa_base_repository_0100 is the dependent repository.
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
# The repository named package_bwa_0_5_9_0100 is the required repository.
tool_repository = self._get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
url = self.url
name = "package_bwa_0_5_9_0100"
owner = "invalid_owner!?"
changeset_revision = self.get_repository_tip(tool_repository)
strings_displayed = ["because the owner is invalid."]
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(
repository=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=True,
package="bwa",
version="0.5.9",
)
[docs]
def test_0030_generate_complex_repository_dependency_invalid_changeset_revision(self):
"""Generate and upload a complex repository definition that specifies an invalid changeset revision."""
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "invalid"])
# The base_repository named bwa_base_repository_0100 is the dependent repository.
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
# The repository named package_bwa_0_5_9_0100 is the required repository.
url = self.url
name = "package_bwa_0_5_9_0100"
owner = "user1"
changeset_revision = "1234abcd"
strings_displayed = ["because the changeset revision is invalid."]
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(
repository=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=True,
package="bwa",
version="0.5.9",
)
[docs]
def test_0035_generate_complex_repository_dependency(self):
"""Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100."""
# The base_repository named bwa_base_repository_0100 is the dependent repository.
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
# The repository named package_bwa_0_5_9_0100 is the required repository.
tool_repository = self._get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex"])
url = self.url
name = "package_bwa_0_5_9_0100"
owner = "user1"
changeset_revision = self.get_repository_tip(tool_repository)
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(
repository=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
complex=True,
package="bwa",
version="0.5.9",
)
self.check_repository_dependency(base_repository, depends_on_repository=tool_repository)
if not self.is_v2:
self.display_manage_repository_page(
base_repository, strings_displayed=["bwa", "0.5.9", "package", changeset_revision]
)