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Source code for tool_shed.test.functional.test_0100_complex_repository_dependencies

import logging
import os

from ..base.twilltestcase import (
    common,
    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) 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.""" 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_id=self.security.encode_id(category.id), strings_displayed=[], ) self.upload_file( repository, filename="bwa/complex/tool_dependencies.xml", filepath=None, 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=[], ) # 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_id=self.security.encode_id(category.id), strings_displayed=[], ) # Populate the repository named bwa_base_repository_0100 with a bwa_base tool archive. 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.""" 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.test_db_util.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.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 = "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.test_db_util.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.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 = "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.test_db_util.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.test_db_util.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.test_db_util.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.test_db_util.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.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 = "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) self.display_manage_repository_page( base_repository, strings_displayed=["bwa", "0.5.9", "package", changeset_revision] )
[docs] def test_0040_generate_tool_dependency(self): """Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.""" # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = self.test_db_util.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.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")) # Generate a tool_dependencies.xml file that points to an arbitrary file in the local filesystem. 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. repository_tip = self.get_repository_tip(tool_repository) strings_displayed = ["bwa", "0.5.9", "package"] strings_displayed.append(repository_tip) strings_not_displayed = [previous_changeset] self.display_manage_repository_page( tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) # Visit the manage page of the package_bwa_0_5_9_0100 to confirm the valid tool dependency definition. self.display_manage_repository_page( tool_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) # Visit the manage page of the bwa_base_repository_0100 to confirm the valid tool dependency definition # and the updated changeset revision (updated tip) of the package_bwa_0_5_9_0100 repository is displayed # as the required repository revision. The original revision defined in the previously uploaded # tool_dependencies.xml file will be updated. self.display_manage_repository_page( base_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )