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Source code for tool_shed.test.functional.test_1070_invalid_tool
from ..base.twilltestcase import (
common,
ShedTwillTestCase,
)
repository_name = "bismark_0070"
repository_description = "Galaxy's bismark wrapper"
repository_long_description = "Long description of Galaxy's bismark wrapper"
category_name = "Test 0070 Invalid Tool Revisions"
category_description = "Test 1070 for a repository with an invalid tool."
[docs]class TestFreebayesRepository(ShedTwillTestCase):
"""Test repository with multiple revisions with invalid tools."""
[docs] def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an admin user."""
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_existence_of_repository_and_category(self):
"""Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool."""
self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.populator.get_category_with_name(category_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,
strings_displayed=[],
)
if self.repository_is_new(repository):
self.upload_file(
repository,
filename="bismark/bismark.tar",
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded bismark tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
self.upload_file(
repository,
filename="bismark/bismark_methylation_extractor.xml",
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded an updated tool 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 bismark repository."""
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])
self.preview_repository_in_tool_shed(
repository_name, common.test_user_1_name, strings_displayed=[repository_name]
)
[docs] def test_0015_install_freebayes_repository(self):
"""Install the test 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_1070",
)
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.update_installed_repository_api(installed_repository, verify_no_updates=True)
self._assert_repo_has_invalid_tool_in_file(installed_repository, "bismark_bowtie_wrapper.xml")