Source code for tool_shed.test.functional.test_1150_datatype_converters

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

repository_name = "bed_to_gff_0130"
repository_description = "Converter: BED to GFF"
repository_long_description = "Convert bed to gff"

category_name = "Test 0130 Datatype Converters"
category_description = "Test 0130 Datatype Converters"

"""
1) Install the bed_to_gff_converter repository.
2) Make sure the page section to select a tool panel section is NOT displayed since the tool will not be displayed in the Galaxy tool panel.
3) Make sure the bed_to_gff_converter tool is not displayed in the tool panel.
"""


[docs]class TestDatatypeConverters(ShedTwillTestCase): """Test features related to datatype converters."""
[docs] def test_0000_initiate_users(self): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) assert ( galaxy_admin_user is not None ), f"Problem retrieving user with email {common.admin_email} from the database" self.test_db_util.get_galaxy_private_role(galaxy_admin_user) 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_bed_to_gff_repository(self): """Create and populate bed_to_gff_0130.""" 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 bed_to_gff_0130 owned by user1. repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=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): # Upload bed_to_gff_converter.tar to the repository, if the repository is new. self.upload_file( repository, filename="bed_to_gff_converter/bed_to_gff_converter.tar", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Uploaded bed_to_gff_converter.tar.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0010_install_datatype_converter_to_galaxy(self): """Install bed_to_gff_converter_0130 into the running Galaxy instance. We are at step 1 - Install the bed_to_gff_converter repository. Install bed_to_gff_converter_0130, checking that the option to select the tool panel section is *not* displayed. """ self.galaxy_login(email=common.admin_email, username=common.admin_username) repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name) preview_strings_displayed = [repository.name, self.get_repository_tip(repository)] strings_displayed = ["Your Galaxy instance is configured with", "shed-related tool configuration file"] strings_not_displayed = ["tool panel section"] self.install_repository( repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, preview_strings_displayed=preview_strings_displayed, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed, post_submit_strings_displayed=[repository.name, "New"], includes_tools_for_display_in_tool_panel=False, )
[docs] def test_0015_uninstall_and_verify_tool_panel_section(self): """Uninstall bed_to_gff_converter_0130 and verify that the saved tool_panel_section is None. We are at step 3 - Make sure the bed_to_gff_converter tool is not displayed in the tool panel. The previous tool panel section for a tool is only recorded in the metadata when a repository is uninstalled, so we have to uninstall it first, then verify that it was not assigned a tool panel section. """ repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name) self.uninstall_repository(repository) self.verify_installed_repository_no_tool_panel_section(repository)