Source code for tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies

import logging
import os

from ..base.twilltestcase import (
    common,
    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 ToolWithToolDependencies(ShedTwillTestCase):
    """Test installing a repository with tool dependencies."""

[docs]    def test_0000_initiate_users(self):
        """Create necessary user accounts."""
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        admin_user = self.test_db_util.get_galaxy_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_galaxy_private_role(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_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_id=self.security.encode_id(category.id),
        )
        if self.repository_is_new(repository):
            self.upload_file(
                repository,
                filename="freebayes/freebayes.xml",
                filepath=None,
                valid_tools_only=False,
                uncompress_file=False,
                remove_repo_files_not_in_tar=False,
                commit_message="Uploaded the tool xml.",
                strings_displayed=[
                    "Metadata may have been defined",
                    "This file requires an entry",
                    "tool_data_table_conf",
                ],
                strings_not_displayed=[],
            )
            self.upload_file(
                repository,
                filename="freebayes/tool_data_table_conf.xml.sample",
                filepath=None,
                valid_tools_only=False,
                uncompress_file=False,
                remove_repo_files_not_in_tar=False,
                commit_message="Uploaded the tool data table sample file.",
                strings_displayed=[],
                strings_not_displayed=[],
            )
            self.upload_file(
                repository,
                filename="freebayes/sam_fa_indices.loc.sample",
                filepath=None,
                valid_tools_only=True,
                uncompress_file=False,
                remove_repo_files_not_in_tar=False,
                commit_message="Uploaded tool data table .loc file.",
                strings_displayed=[],
                strings_not_displayed=[],
            )
            self.upload_file(
                repository,
                filename=os.path.join("freebayes", "malformed_tool_dependencies", "tool_dependencies.xml"),
                filepath=None,
                valid_tools_only=False,
                uncompress_file=False,
                remove_repo_files_not_in_tar=False,
                commit_message="Uploaded malformed tool dependency XML.",
                strings_displayed=["Exception attempting to parse", "not well-formed"],
                strings_not_displayed=[],
            )
            self.upload_file(
                repository,
                filename=os.path.join("freebayes", "invalid_tool_dependencies", "tool_dependencies.xml"),
                filepath=None,
                valid_tools_only=False,
                uncompress_file=False,
                remove_repo_files_not_in_tar=False,
                commit_message="Uploaded invalid tool dependency XML.",
                strings_displayed=[
                    "The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration"
                ],
                strings_not_displayed=[],
            )
            self.upload_file(
                repository,
                filename=os.path.join("freebayes", "tool_dependencies.xml"),
                filepath=None,
                valid_tools_only=True,
                uncompress_file=False,
                remove_repo_files_not_in_tar=False,
                commit_message="Uploaded valid tool dependency 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 freebayes tool."""
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        self.browse_tool_shed(url=self.url, strings_displayed=[category_name])
        category = self.test_db_util.get_category_by_name(category_name)
        self.browse_category(category, strings_displayed=[repository_name])
        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."""
        strings_displayed = [
            "Never installed",
            "install all needed dependencies",
        ]
        strings_displayed.extend(["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18"])
        self.install_repository(
            repository_name,
            common.test_user_1_name,
            category_name,
            strings_displayed=strings_displayed,
            install_tool_dependencies=False,
            new_tool_panel_section_label="test_1010",
        )
        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
            repository_name, common.test_user_1_name
        )
        strings_displayed = [
            "freebayes_0010",
            "Galaxy's freebayes tool",
            "user1",
            self.url.replace("http://", ""),
            installed_repository.installed_changeset_revision,
        ]
        self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
        strings_displayed.extend(["Installed tool shed repository", "Valid tools", "FreeBayes"])
        self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
        self.verify_tool_metadata_for_installed_repository(installed_repository)

[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"])