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)