Source code for tool_shed.test.functional.test_1170_prior_installation_required

import logging

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

log = logging.getLogger(__name__)

column_repository_name = "column_maker_0150"
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"

convert_repository_name = "convert_chars_0150"
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"

category_name = "Test 0150 Simple Prior Installation"
category_description = "Test 0150 Simple Prior Installation"

"""
Create column_maker and convert_chars.

Column maker repository dependency:
<repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />

Verify display.

Galaxy side:

Install column_maker.
Verify that convert_chars was installed first, contrary to the ordering that would be present without prior_installation_required.
"""

running_standalone = False


[docs]class TestSimplePriorInstallation(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_convert_repository(self):
        """Create and populate convert_chars_0150."""
        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=convert_repository_name,
            description=convert_repository_description,
            long_description=convert_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):
            running_standalone = True
            self.upload_file(
                repository,
                filename="convert_chars/convert_chars.tar",
                filepath=None,
                valid_tools_only=True,
                uncompress_file=True,
                remove_repo_files_not_in_tar=False,
                commit_message="Uploaded convert_chars tarball.",
                strings_displayed=[],
                strings_not_displayed=[],
            )

[docs]    def test_0010_create_column_repository(self):
        """Create and populate convert_chars_0150."""
        global running_standalone
        category = self.create_category(name=category_name, description=category_description)
        repository = self.get_or_create_repository(
            name=column_repository_name,
            description=column_repository_description,
            long_description=column_repository_long_description,
            owner=common.test_user_1_name,
            category_id=self.security.encode_id(category.id),
            strings_displayed=[],
        )
        if running_standalone:
            self.upload_file(
                repository,
                filename="column_maker/column_maker.tar",
                filepath=None,
                valid_tools_only=True,
                uncompress_file=True,
                remove_repo_files_not_in_tar=False,
                commit_message="Uploaded column_maker tarball.",
                strings_displayed=[],
                strings_not_displayed=[],
            )

[docs]    def test_0015_create_repository_dependency(self):
        """Create a repository dependency specifying convert_chars.

        Column maker repository dependency:
            <repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="<tip>" prior_installation_required="True" />
        """
        global running_standalone
        column_repository = self.test_db_util.get_repository_by_name_and_owner(
            column_repository_name, common.test_user_1_name
        )
        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
            convert_repository_name, common.test_user_1_name
        )
        if running_standalone:
            dependency_xml_path = self.generate_temp_path("test_1150", additional_paths=["column"])
            convert_tuple = (
                self.url,
                convert_repository.name,
                convert_repository.user.username,
                self.get_repository_tip(convert_repository),
            )
            self.create_repository_dependency(
                repository=column_repository,
                repository_tuples=[convert_tuple],
                filepath=dependency_xml_path,
                prior_installation_required=True,
            )

[docs]    def test_0020_verify_repository_dependency(self):
        """Verify that the previously generated repositiory dependency displays correctly."""
        column_repository = self.test_db_util.get_repository_by_name_and_owner(
            column_repository_name, common.test_user_1_name
        )
        convert_repository = self.test_db_util.get_repository_by_name_and_owner(
            convert_repository_name, common.test_user_1_name
        )
        self.check_repository_dependency(
            repository=column_repository,
            depends_on_repository=convert_repository,
            depends_on_changeset_revision=None,
            changeset_revision=None,
        )

[docs]    def test_0025_install_column_repository(self):
        """Install column_maker_0150."""
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        column_repository = self.test_db_util.get_repository_by_name_and_owner(
            column_repository_name, common.test_user_1_name
        )
        preview_strings_displayed = ["column_maker_0150", self.get_repository_tip(column_repository)]
        strings_displayed = ["Choose the tool panel section"]
        self.install_repository(
            column_repository_name,
            common.test_user_1_name,
            category_name,
            install_tool_dependencies=False,
            install_repository_dependencies=True,
            preview_strings_displayed=preview_strings_displayed,
            strings_displayed=strings_displayed,
            strings_not_displayed=[],
            post_submit_strings_displayed=["column_maker_0150", "New"],
            includes_tools_for_display_in_tool_panel=True,
        )

[docs]    def test_0030_verify_installation_order(self):
        """Verify that convert_chars_0150 was installed before column_maker_0150."""
        column_repository = self.test_db_util.get_installed_repository_by_name_owner(
            column_repository_name, common.test_user_1_name
        )
        convert_repository = self.test_db_util.get_installed_repository_by_name_owner(
            convert_repository_name, common.test_user_1_name
        )
        # Column maker was selected for installation, so convert chars should have been installed first, as reflected by the update_time field.
        assert (
            column_repository.update_time > convert_repository.update_time
        ), "Error: column_maker_0150 shows an earlier update time than convert_chars_0150"