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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 TestToolWithToolDependencies(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", "invalid element name"],
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."""
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.test_db_util.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"])