def test_maximum_length_handling_ascii():
# Test that id secrets can be up to 56 characters long.
longest_id_secret = "m" * idencoding.MAXIMUM_ID_SECRET_LENGTH
helper = idencoding.IdEncodingHelper(id_secret=longest_id_secret)
helper.encode_id(1)
# Test that security helper will catch if the id secret is too long.
threw_exception = False
longer_id_secret = "m" * (idencoding.MAXIMUM_ID_SECRET_LENGTH + 1)
try:
idencoding.IdEncodingHelper(id_secret=longer_id_secret)
except Exception:
threw_exception = True
assert threw_exception
# Test that different kinds produce different keys even when id secret
# is very long.
e11 = helper.encode_id(1, kind="moo")
e12 = helper.encode_id(1, kind="moo2")
assert e11 != e12
# Test that long kinds are rejected because it uses up "too much" randomness
# from id_secret values. This isn't a strict requirement up but lets just enforce
# the best practice.
assertion_error_raised = False
try:
helper.encode_id(1, kind="this is a really long kind")
except AssertionError:
assertion_error_raised = True
assert assertion_error_raised
def __init__(self, **kwargs):
super().__init__()
self[BasicApp] = self
log.debug("python path is: %s", ", ".join(sys.path))
self.name = "reports"
# Read config file and check for errors
self.config = config.Configuration(**kwargs)
self.config.check()
configure_logging(self.config)
self.application_stack = application_stack_instance()
# Determine the database url
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Setup the database engine and ORM
self.model = galaxy.model.mapping.init(
self.config.file_path,
db_url,
self.config.database_engine_options,
create_tables=True)
if not self.config.database_connection:
self.targets_mysql = False
else:
self.targets_mysql = 'mysql' in self.config.database_connection
# Security helper
self.security = idencoding.IdEncodingHelper(
id_secret=self.config.id_secret)
self._register_singleton(idencoding.IdEncodingHelper, self.security)
self._register_singleton(SharedModelMapping, self.model)
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
self.server_starttime = int(time.time())
def setUp(self):
self.security = idencoding.IdEncodingHelper(
id_secret='changethisinproductiontoo')
self.history_id = os.environ.get('GALAXY_TEST_HISTORY_ID', None)
self.host, self.port, self.url = target_url_parts()
self.test_data_resolver = TestDataResolver()
self.keepOutdir = setup_keep_outdir()
def __init__(self, **kwargs):
log.debug("python path is: %s", ", ".join(sys.path))
self.name = "coralsnp_reports"
# Read config file and check for errors
self.config = config.Configuration(**kwargs)
self.config.check()
config.configure_logging(self.config)
self.application_stack = application_stack_instance()
# Determine the database url
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "postgresql://*****:*****@localhost/stag"
# Setup the database engine and ORM
self.model = galaxy.model.corals.mapping.init(
db_url, self.config.database_engine_options)
if not self.config.database_connection:
self.targets_mysql = False
else:
self.targets_mysql = 'mysql' in self.config.database_connection
# Security helper
self.security = idencoding.IdEncodingHelper(
id_secret=self.config.id_secret)
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
self.server_starttime = int(time.time())
def __init__(self, **kwd):
log.debug("python path is: %s", ", ".join(sys.path))
self.name = "tool_shed"
# Read the tool_shed.ini configuration file and check for errors.
self.config = config.Configuration(**kwd)
self.config.check()
configure_logging(self.config)
self.application_stack = application_stack_instance()
# Initialize the Galaxy datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes(self.config.root,
self.config.datatypes_config)
# Initialize the Tool Shed repository_types registry.
self.repository_types_registry = tool_shed.repository_types.registry.Registry(
)
# Initialize the RepositoryGridFilterManager.
self.repository_grid_filter_manager = RepositoryGridFilterManager()
# Determine the Tool Shed database connection string.
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Initialize the Tool Shed database and check for appropriate schema version.
from galaxy.webapps.tool_shed.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, self.config.database_engine_options)
# Set up the Tool Shed database engine and ORM.
from galaxy.webapps.tool_shed.model import mapping
self.model = mapping.init(self.config.file_path, db_url,
self.config.database_engine_options)
self.security = idencoding.IdEncodingHelper(
id_secret=self.config.id_secret)
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagHandler(self)
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
self.config.tool_data_path)
self.genome_builds = GenomeBuilds(self)
from galaxy import auth
self.auth_manager = auth.AuthManager(self)
# Citation manager needed to load tools.
from galaxy.managers.citations import CitationsManager
self.citations_manager = CitationsManager(self)
# The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required.
self.toolbox = tools.ToolBox([], self.config.tool_path, self)
# Initialize the Tool Shed security agent.
self.security_agent = self.model.security_agent
# The Tool Shed makes no use of a quota, but this attribute is still required.
self.quota_agent = galaxy.quota.NoQuotaAgent(self.model)
# Initialize the baseline Tool Shed statistics component.
self.shed_counter = self.model.shed_counter
# Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
self.hgweb_config_manager = self.model.hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry(self)
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
self.server_starttime = int(time.time())
log.debug("Tool shed hgweb.config file is: %s",
self.hgweb_config_manager.hgweb_config)
def __init__(self, root=None, **kwargs):
Bunch.__init__(self, **kwargs)
if not root:
root = tempfile.mkdtemp()
self._remove_root = True
else:
self._remove_root = False
self.security = idencoding.IdEncodingHelper(
id_secret='6e46ed6483a833c100e68cc3f1d0dd76')
self.database_connection = kwargs.get('database_connection',
"sqlite:///:memory:")
self.use_remote_user = kwargs.get('use_remote_user', False)
self.data_dir = os.path.join(root, 'database')
self.file_path = os.path.join(self.data_dir, 'files')
self.jobs_directory = os.path.join(self.data_dir, 'jobs_directory')
self.new_file_path = os.path.join(self.data_dir, 'tmp')
self.tool_data_path = os.path.join(root, 'tool-data')
self.tool_dependency_dir = None
self.metadata_strategy = 'legacy'
self.object_store_config_file = ''
self.object_store = 'disk'
self.object_store_check_old_style = False
self.object_store_cache_path = '/tmp/cache'
self.umask = os.umask(0o77)
self.gid = os.getgid()
self.user_activation_on = False
self.new_user_dataset_access_role_default_private = False
self.expose_dataset_path = True
self.allow_user_dataset_purge = True
self.enable_old_display_applications = True
self.redact_username_in_logs = False
self.auth_config_file = "config/auth_conf.xml.sample"
self.error_email_to = "*****@*****.**"
self.password_expiration_period = 0
self.umask = 0o77
# Compliance related config
self.redact_email_in_job_name = False
# Follow two required by GenomeBuilds
self.len_file_path = os.path.join('tool-data', 'shared', 'ucsc',
'chrom')
self.builds_file_path = os.path.join('tool-data', 'shared', 'ucsc',
'builds.txt.sample')
self.preserve_python_environment = "always"
self.enable_beta_gdpr = False
self.legacy_eager_objectstore_initialization = True
self.version_major = "19.09"
# set by MockDir
self.root = root
self.config_file = None
def test_maximum_length_handling_nonascii():
longest_id_secret = "◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎"
helper = idencoding.IdEncodingHelper(id_secret=longest_id_secret)
helper.encode_id(1)
# Test that security helper will catch if the id secret is too long.
threw_exception = False
longer_id_secret = "◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎◎"
try:
idencoding.IdEncodingHelper(id_secret=longer_id_secret)
except Exception:
threw_exception = True
assert threw_exception
# Test that different kinds produce different keys even when id secret
# is very long.
e11 = helper.encode_id(1, kind="moo")
e12 = helper.encode_id(1, kind="moo2")
assert e11 != e12
import galaxy.config
from galaxy.security import idencoding
from galaxy.util.script import app_properties_from_args, populate_config_args
parser = argparse.ArgumentParser()
populate_config_args(parser)
parser.add_argument('-e', '--encode-id', dest='encode_id', help='Encode an ID')
parser.add_argument('-d', '--decode-id', dest='decode_id', help='Decode an ID')
parser.add_argument('--hda', dest='hda_id', help='Display HistoryDatasetAssociation info')
parser.add_argument('--ldda', dest='ldda_id', help='Display LibraryDatasetDatasetAssociation info')
args = parser.parse_args()
app_properties = app_properties_from_args(args)
config = galaxy.config.Configuration(**app_properties)
helper = idencoding.IdEncodingHelper(id_secret=app_properties.get('id_secret'))
model = galaxy.config.init_models_from_config(config)
if args.encode_id:
print('Encoded "{}": {}'.format(args.encode_id, helper.encode_id(args.encode_id)))
if args.decode_id:
print('Decoded "{}": {}'.format(args.decode_id, helper.decode_id(args.decode_id)))
if args.hda_id:
try:
hda_id = int(args.hda_id)
except Exception:
hda_id = int(helper.decode_id(args.hda_id))
hda = model.context.current.query(model.HistoryDatasetAssociation).get(hda_id)
print(f'HDA "{hda.id}" is Dataset "{hda.dataset.id}" at: {hda.file_name}')
def __init__(self, **kwargs):
self.name = kwargs.get('name', 'galaxy')
self.security = idencoding.IdEncodingHelper(
id_secret='6e46ed6483a833c100e68cc3f1d0dd76')
from galaxy.security import idencoding
test_helper_1 = idencoding.IdEncodingHelper(id_secret="secu1")
test_helper_2 = idencoding.IdEncodingHelper(id_secret="secu2")
def test_maximum_length_handling_ascii():
# Test that id secrets can be up to 56 characters long.
longest_id_secret = "m" * idencoding.MAXIMUM_ID_SECRET_LENGTH
helper = idencoding.IdEncodingHelper(id_secret=longest_id_secret)
helper.encode_id(1)
# Test that security helper will catch if the id secret is too long.
threw_exception = False
longer_id_secret = "m" * (idencoding.MAXIMUM_ID_SECRET_LENGTH + 1)
try:
idencoding.IdEncodingHelper(id_secret=longer_id_secret)
except Exception:
threw_exception = True
assert threw_exception
# Test that different kinds produce different keys even when id secret
# is very long.
e11 = helper.encode_id(1, kind="moo")
e12 = helper.encode_id(1, kind="moo2")
assert e11 != e12
# Test that long kinds are rejected because it uses up "too much" randomness
# from id_secret values. This isn't a strict requirement up but lets just enforce
def __init__(self, **kwd) -> None:
super().__init__()
self[BasicApp] = self
log.debug("python path is: %s", ", ".join(sys.path))
self.name = "tool_shed"
# will be overwritten when building WSGI app
self.is_webapp = False
# Read the tool_shed.ini configuration file and check for errors.
self.config: Any = config.Configuration(**kwd)
self.config.check()
configure_logging(self.config)
self.application_stack = application_stack_instance()
# Initialize the Galaxy datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes(self.config.root,
self.config.datatypes_config)
# Initialize the Tool Shed repository_types registry.
self.repository_types_registry = tool_shed.repository_types.registry.Registry(
)
# Initialize the RepositoryGridFilterManager.
self.repository_grid_filter_manager = RepositoryGridFilterManager()
# Determine the Tool Shed database connection string.
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = f"sqlite:///{self.config.database}?isolation_level=IMMEDIATE"
# Initialize the Tool Shed database and check for appropriate schema version.
from tool_shed.webapp.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, self.config.database_engine_options)
# Set up the Tool Shed database engine and ORM.
from tool_shed.webapp.model import mapping
model: mapping.ToolShedModelMapping = mapping.init(
self.config.file_path, db_url, self.config.database_engine_options)
self.model = model
self.security = idencoding.IdEncodingHelper(
id_secret=self.config.id_secret)
self._register_singleton(idencoding.IdEncodingHelper, self.security)
self._register_singleton(SharedModelMapping, model)
self._register_singleton(mapping.ToolShedModelMapping, model)
self._register_singleton(scoped_session, self.model.context)
self._register_singleton(UserManager, UserManager)
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagHandler(self)
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
self.config.tool_data_path)
self.genome_builds = GenomeBuilds(self)
self.auth_manager = self._register_singleton(
auth.AuthManager, auth.AuthManager(self.config))
# Citation manager needed to load tools.
self.citations_manager = self._register_singleton(
CitationsManager, CitationsManager(self))
self.use_tool_dependency_resolution = False
# Initialize the Tool Shed security agent.
self.security_agent = model.security_agent
# The Tool Shed makes no use of a quota, but this attribute is still required.
self.quota_agent = self._register_singleton(QuotaAgent, NoQuotaAgent())
# Initialize the baseline Tool Shed statistics component.
self.shed_counter = model.shed_counter
# Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
self.hgweb_config_manager = hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry(self)
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
self.server_starttime = int(time.time())
log.debug("Tool shed hgweb.config file is: %s",
self.hgweb_config_manager.hgweb_config)
