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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) 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.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.populator.get_category_with_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"])