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Source code for tool_shed.test.functional.test_1070_invalid_tool

from ..base.twilltestcase import (
    common,
    ShedTwillTestCase,
)

repository_name = "bismark_0070"
repository_description = "Galaxy's bismark wrapper"
repository_long_description = "Long description of Galaxy's bismark wrapper"
category_name = "Test 0070 Invalid Tool Revisions"
category_description = "Test 1070 for a repository with an invalid tool."


[docs]class TestFreebayesRepository(ShedTwillTestCase): """Test repository with multiple revisions with invalid tools."""
[docs] def test_0000_create_or_login_admin_user(self): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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_ensure_existence_of_repository_and_category(self): """Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.""" self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, category=category, strings_displayed=[], ) if self.repository_is_new(repository): self.upload_file( repository, filename="bismark/bismark.tar", filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded bismark tarball.", strings_displayed=[], strings_not_displayed=[], ) self.upload_file( repository, filename="bismark/bismark_methylation_extractor.xml", filepath=None, valid_tools_only=False, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Uploaded an updated tool xml.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0010_browse_tool_shed(self): """Browse the available tool sheds in this Galaxy instance and preview the bismark repository.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) self.browse_tool_shed(url=self.url, strings_displayed=[category_name]) category = self.populator.get_category_with_name(category_name) self.browse_category(category, strings_displayed=[repository_name]) self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=[repository_name] )
[docs] def test_0015_install_freebayes_repository(self): """Install the test repository without installing tool dependencies.""" self.install_repository( repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, new_tool_panel_section_label="test_1070", ) installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) strings_displayed = [ "bismark_0070", "Galaxy's bismark wrapper", "user1", self.url.replace("http://", ""), installed_repository.installed_changeset_revision, ] self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed) strings_displayed.extend(["methylation extractor", "Invalid tools"]) self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed, strings_not_displayed=["bisulfite mapper"] ) self.verify_tool_metadata_for_installed_repository(installed_repository) self.update_installed_repository(installed_repository, strings_displayed=["there are no updates available"]) assert "invalid_tools" in installed_repository.metadata_, ( "No invalid tools were defined in %s." % installed_repository.name )