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Source code for tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies
import os
from ..base.twilltestcase import (
common,
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."""
[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)
[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_id=self.security.encode_id(category.id),
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.upload_file(
repository,
filename=xml_filename,
filepath=new_tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded tool_dependencies.xml.",
strings_displayed=[
"This repository currently contains a single file named <b>tool_dependencies.xml</b>"
],
strings_not_displayed=[],
)
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_id=self.security.encode_id(category.id),
strings_displayed=[],
)
self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
self.upload_file(
repository,
filename="bwa/complex/bwa_base.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.",
strings_displayed=[],
strings_not_displayed=[],
)
[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.test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = self.test_db_util.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.user.username
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.test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = self.test_db_util.get_repository_by_name_and_owner(
bwa_package_repository_name, common.test_user_1_name
)
url = self.url
name = "invalid_repository!?"
owner = tool_repository.user.username
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.test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = self.test_db_util.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.test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = self.test_db_util.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.user.username
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.test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = self.test_db_util.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.user.username
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_0040_update_tool_repository(self):
"""Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset."""
global running_standalone
if running_standalone:
base_repository = self.test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = self.test_db_util.get_repository_by_name_and_owner(
bwa_package_repository_name, common.test_user_1_name
)
previous_changeset = self.get_repository_tip(tool_repository)
old_tool_dependency = self.get_filename(os.path.join("bwa", "complex", "readme", "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.upload_file(
tool_repository,
filename=xml_filename,
filepath=new_tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded new tool_dependencies.xml.",
strings_displayed=[],
strings_not_displayed=[],
)
# Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file.
self.display_manage_repository_page(
base_repository,
strings_displayed=[self.get_repository_tip(tool_repository), "bwa", "0.5.9", "package"],
strings_not_displayed=[previous_changeset],
)
[docs] def test_0045_install_base_repository(self):
"""Verify installation of the repository with complex repository dependencies."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
base_repository = self.test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = self.test_db_util.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,
install_tool_dependencies=True,
preview_strings_displayed=preview_strings_displayed,
post_submit_strings_displayed=[base_repository.name, tool_repository.name, "New"],
includes_tools_for_display_in_tool_panel=True,
)
[docs] def test_0050_verify_installed_repositories(self):
"""Verify that the installed repositories are displayed properly."""
base_repository = self.test_db_util.get_installed_repository_by_name_owner(
bwa_base_repository_name, common.test_user_1_name
)
tool_repository = self.test_db_util.get_installed_repository_by_name_owner(
bwa_package_repository_name, common.test_user_1_name
)
strings_displayed = ["bwa_base_repository_0100", "user1", base_repository.installed_changeset_revision]
strings_displayed.extend(["package_bwa_0_5_9_0100", "user1", tool_repository.installed_changeset_revision])
strings_displayed.append(self.url.replace("http://", ""))
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed, strings_not_displayed=[])
strings_displayed = ["package_bwa_0_5_9_0100", "user1", tool_repository.installed_changeset_revision]
strings_not_displayed = ["Missing tool dependencies"]
self.display_installed_repository_manage_page(
tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
)
strings_displayed = [
"bwa_base_repository_0100",
"user1",
"package_bwa_0_5_9_0100",
base_repository.installed_changeset_revision,
tool_repository.installed_changeset_revision,
]
strings_not_displayed = ["Missing tool dependencies"]
self.display_installed_repository_manage_page(
base_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed
)