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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) 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.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=category, strings_displayed=[], ) self._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._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_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._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 ) 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) 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, install_tool_dependencies=True, 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.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 )