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"])