Source code for tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies

import logging

from ..base import common
from ..base.twilltestcase import ShedTwillTestCase

repository_name = "freebayes_0010"
repository_description = "Galaxy's freebayes tool"
repository_long_description = "Long description of Galaxy's freebayes tool"
category_name = "Test 0010 Repository With Tool Dependencies"
log = logging.getLogger(__name__)


[docs]class TestToolWithToolDependencies(ShedTwillTestCase):
    """Test installing a repository with tool dependencies."""

    requires_galaxy = True

[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_ensure_repositories_and_categories_exist(self):
        """Create the 0010 category and upload the freebayes repository to it, if necessary."""
        category = self.create_category(
            name=category_name, description="Tests for a repository with tool dependencies."
        )
        self.login(email=common.test_user_1_email, username=common.test_user_1_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,
        )
        if self.repository_is_new(repository):
            self.setup_freebayes_0010_repo(repository)

[docs]    def test_0010_browse_tool_shed(self):
        """Browse the available tool sheds in this Galaxy instance and preview the freebayes tool."""
        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])
        if not self.is_v2:
            strings_displayed = [repository_name, "Valid tools", "Tool dependencies"]
            self.preview_repository_in_tool_shed(
                repository_name, common.test_user_1_name, strings_displayed=strings_displayed
            )

[docs]    def test_0015_install_freebayes_repository(self):
        """Install the freebayes 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_1010",
        )
        installed_repository = self._get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
        assert self._get_installed_repository_for(
            common.test_user_1, repository_name, installed_repository.installed_changeset_revision
        )
        self._assert_has_valid_tool_with_name("FreeBayes")
        self._assert_repo_has_tool_with_id(installed_repository, "freebayes")

[docs]    def test_0020_verify_installed_repository_metadata(self):
        """Verify that resetting the metadata on an installed repository does not change the metadata."""
        self.verify_installed_repository_metadata_unchanged(repository_name, common.test_user_1_name)

[docs]    def test_0025_verify_sample_files(self):
        """Verify that the installed repository populated shed_tool_data_table.xml and the sample files."""
        self.verify_installed_repository_data_table_entries(required_data_table_entries=["sam_fa_indexes"])