import os
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
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 Package"
bwa_package_repository_long_description = (
"BWA repository with a package tool dependency defined to compile and install BWA 0.5.9."
)
category_name = "Test 0100 Complex Repository Dependencies"
category_description = "Test 0100 Complex Repository Dependencies"
running_standalone = False
[docs]class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase):
"""Test features related to installing repositories with complex repository dependencies."""
requires_galaxy = True
[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)
[docs] def test_0005_create_bwa_package_repository(self):
"""Create and populate package_bwa_0_5_9_0100."""
global running_standalone
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_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=[],
)
if self.repository_is_new(repository):
running_standalone = True
old_tool_dependency = self.get_filename(os.path.join("bwa", "complex", "tool_dependencies.xml"))
new_tool_dependency_path = self.generate_temp_path("test_1100", additional_paths=["tool_dependency"])
xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, "tool_dependencies.xml"))
open(xml_filename, "w").write(
open(old_tool_dependency).read().replace("__PATH__", self.get_filename("bwa/complex"))
)
self.add_file_to_repository(repository, xml_filename, "tool_dependencies.xml")
self.display_manage_repository_page(
repository, strings_displayed=["Tool dependencies", "consider setting its type"]
)
[docs] def test_0010_create_bwa_base_repository(self):
"""Create and populate bwa_base_0100."""
global running_standalone
if running_standalone:
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=category,
strings_displayed=[],
)
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."""
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "shed"])
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
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 = tool_repository.name
owner = tool_repository.owner
changeset_revision = self.get_repository_tip(tool_repository)
strings_displayed = ["Repository dependencies are currently supported only within the same tool shed"]
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."""
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "shed"])
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
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 = tool_repository.owner
changeset_revision = self.get_repository_tip(tool_repository)
strings_displayed = ["because the name 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_0025_generate_complex_repository_dependency_invalid_owner_name(self):
"""Generate and upload a complex repository definition that specifies an invalid owner."""
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "shed"])
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self._get_repository_by_name_and_owner(
bwa_package_repository_name, common.test_user_1_name
)
url = self.url
name = tool_repository.name
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."""
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path("test_0100", additional_paths=["complex", "shed"])
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self._get_repository_by_name_and_owner(
bwa_package_repository_name, common.test_user_1_name
)
url = self.url
name = tool_repository.name
owner = tool_repository.owner
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_valid_complex_repository_dependency(self):
"""Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100."""
global running_standalone
if running_standalone:
base_repository = self._get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
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 = tool_repository.name
owner = tool_repository.owner
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, tool_repository)
self.display_manage_repository_page(base_repository, strings_displayed=["bwa", "0.5.9", "package"])
[docs] def test_0045_install_base_repository(self):
"""Verify installation of the repository with complex repository dependencies."""
tool_repository = self._get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
preview_strings_displayed = [tool_repository.name, self.get_repository_tip(tool_repository)]
self._install_repository(
bwa_base_repository_name,
common.test_user_1_name,
category_name,
preview_strings_displayed=preview_strings_displayed,
)
[docs] def test_0050_verify_installed_repositories(self):
"""Verify that the installed repositories are displayed properly."""
base_repository = self._get_installed_repository_by_name_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = self._get_installed_repository_by_name_owner(
bwa_package_repository_name, common.test_user_1_name
)
assert self._get_installed_repository_for(
common.test_user_1, "bwa_base_repository_0100", base_repository.installed_changeset_revision
)
assert self._get_installed_repository_for(
common.test_user_1, "package_bwa_0_5_9_0100", tool_repository.installed_changeset_revision
)
self._assert_has_installed_repository_dependency(base_repository, "package_bwa_0_5_9_0100")