def setup():
global _log, services
_log = get_logger("doekbase.data_api.tests.shared")
services = get_services()
if services["redis_host"] is not None:
cache.ObjectCache.cache_class = cache.RedisCache
cache.ObjectCache.cache_params = {"redis_host": services["redis_host"], "redis_port": services["redis_port"]}
def setup():
global _log, services
_log = get_logger('doekbase.data_api.tests.shared')
services = get_services()
if services["redis_host"] is not None:
cache.ObjectCache.cache_class = cache.RedisCache
cache.ObjectCache.cache_params = {
'redis_host': services["redis_host"],
'redis_port': services["redis_port"]
}
## Imports
# System
import hashlib
import logging
import os
import time
import uuid
# Third-party
from dogpile.cache import make_region
import redis
# Local
from doekbase.data_api.util import PerfCollector, get_logger
_log = get_logger(__name__)
## Functions and Classes
class Cache(object):
def __init__(self):
self.region = None
def __getattr__(self, item):
return getattr(self.region, item)
class RedisCache(Cache):
def __init__(self, **kwargs):
super(self.__class__, self).__init__()
def setup():
global _log, services
_log = get_logger('doekbase.data_api.tests.shared')
services = get_services()
import qgrid
qgrid.nbinstall()
except ImportError:
qgrid = None
from jinja2 import Template
# Seaborn graphing
try:
import seaborn as sns
sns.set_style("whitegrid")
except ImportError:
sns = None
# Local
from doekbase.data_api.util import get_logger, log_start, log_end
_log = get_logger('doekbase.data_api.display')
_nbviewer = False
def nbviewer_mode(value=None):
"""Get/set the global nbviewer-friendly mode.
This is currently used to tell qgrid where to get
its JavaScript from (local or a CDN).
"""
global _nbviewer
if value is not None:
_nbviewer = bool(value)
return _nbviewer
# Imports
# Stdlib
import json
try:
import cStringIO as StringIO
except ImportError:
import StringIO as StringIO
# Local
import doekbase.workspace.client
from . import thrift_service, ttypes
from doekbase.data_api.util import get_logger, log_start, log_end
from doekbase.data_api.rpc_util import thrift_validate
_log = get_logger('baseobj.impl')
class ObjectImpl(thrift_service.Iface):
def __init__(self, services=None):
print("IN ObjectImpl")
if services is None or type(services) != type({}):
raise TypeError("You must provide a service configuration "
"dictionary! Found {0}".format(type(services)))
elif not services.has_key("workspace_service_url"):
raise KeyError("Expecting workspace_service_url key!")
self.services = services
self.ws_client = None
self.ref = None
def init(self, auth):
import os
import re
try:
import cStringIO as StringIO
except ImportError:
import StringIO as StringIO
# Local
from doekbase.data_api.util import get_logger, log_start, log_end
from doekbase.workspace.client import Workspace
from doekbase.data_api.wsfile import WorkspaceFile
from doekbase.data_api import cache
from doekbase.data_api.util import PerfCollector, collect_performance
# Logging
_log = get_logger('doekbase.data_api.core')
# Globals
REF_PATTERN = re.compile("(.+/.+(/[0-9].+)?)|(ws\.[1-9][0-9]+\.[1-9][0-9]+)")
g_ws_url = "https://ci.kbase.us/services/ws/"
g_shock_url = "https://ci.kbase.us/services/shock-api/"
g_handle_url = "https://ci.kbase.us/services/handle_service/"
g_use_msgpack = True
g_stats = PerfCollector('ObjectAPI')
def fix_docs(cls):
for name, func in vars(cls).items():
if func is not None and func.__doc__ is None:
def setup():
global _log, services
_log = get_logger('doekbase.data_api.tests.shared')
services = get_services()
__date__ = '9/30/15'
# System
import os
import threading
import time
import unittest
# Third-party
from dogpile.cache.api import NO_VALUE
# Local
from doekbase.data_api import cache
from doekbase.data_api import util
from doekbase.data_api.core import ObjectAPI
from . import shared
_log = util.get_logger(__name__)
# Uncomment this line to turn off DBM tests
USE_DBM = False
def setup():
shared.setup()
class TestCache(unittest.TestCase):
"""Test the cache.
"""
dbm_path = None
## Setup / teardown
@classmethod
import twisted.internet
import twisted.web
from thrift.transport import TTwisted
from thrift.protocol import TBinaryProtocol
# Local
from doekbase.data_api.taxonomy.taxon.service import thrift_service
from doekbase.data_api.taxonomy.taxon.service.interface import TaxonService
from doekbase.data_api.util import get_logger
DEFAULT_WS_URL = 'https://ci.kbase.us/services/ws/'
DEFAULT_SHOCK_URL = 'https://ci.kbase.us/services/shock-api/'
# set up a logger for Thrift messages
_log = get_logger('taxon_service')
def get_services_dict(ws=DEFAULT_WS_URL, shock=DEFAULT_SHOCK_URL):
return {'workspace_service_url': ws,
'shock_service_url': shock}
#TODO respond to kill signals
#TODO on HUP reload of config
def start_service(services = None, host = 'localhost', port = 9101):
if services is None:
services = get_services_dict()
handler = TaxonService(services)
processor = thrift_service.Processor(handler)
pfactory = TBinaryProtocol.TBinaryProtocolFactory()
resource = TTwisted.ThriftResource(processor, pfactory, pfactory)
import os
import re
try:
import cStringIO as StringIO
except ImportError:
import StringIO as StringIO
# Local
from doekbase.data_api.util import get_logger, log_start, log_end
from doekbase.workspace.client import Workspace
from doekbase.data_api.wsfile import WorkspaceFile
from doekbase.data_api import cache
from doekbase.data_api.util import PerfCollector, collect_performance
# Logging
_log = get_logger('doekbase.data_api.core')
# Globals
REF_PATTERN = re.compile("(.+/.+(/[0-9].+)?)|(ws\.[1-9][0-9]+\.[1-9][0-9]+)")
g_ws_url = "https://ci.kbase.us/services/ws/"
g_shock_url = "https://ci.kbase.us/services/shock-api/"
g_use_msgpack = True
g_stats = PerfCollector('ObjectAPI')
# Functions and Classes
#: Name positional parts of WorkspaceInfo tuple
WorkspaceInfo = namedtuple('WorkspaceInfo', [
'id', # ws_id (int)
# Imports
# Stdlib
import json
import logging
import re
# Local
from doekbase.data_api.util import get_logger
from doekbase.data_api.util import log_start, log_end
from doekbase.data_api.util import get_auth_token
from . import thrift_service, ttypes
# Logging
_log = get_logger('object_api')
_log.setLevel(logging.DEBUG)
# Constants
NAMESPACE = 'Object'
REF_PATTERN = re.compile("(.+/.+(/[0-9].+)?)|(ws\.[1-9][0-9]+\.[1-9][0-9]+)")
# Classes and functions
class ObjectAPI(object):
"""API layer over the autogenerated Thrift interface.
This can handle both local and remote modes by use of alternate
implementations of the `client` parameter.
except ImportError:
qgrid = None
from jinja2 import Template
# Seaborn graphing
try:
import seaborn as sns
sns.set_style("whitegrid")
except ImportError:
sns = None
# Local
from doekbase.data_api.util import get_logger, log_start, log_end
_log = get_logger("doekbase.data_api.display")
_nbviewer = False
def nbviewer_mode(value=None):
"""Get/set the global nbviewer-friendly mode.
This is currently used to tell qgrid where to get
its JavaScript from (local or a CDN).
"""
global _nbviewer
if value is not None:
_nbviewer = bool(value)
return _nbviewer
"""
Service driver for Assembly API.
"""
# Imports
# -------
# Local
from doekbase.data_api import service_core
from doekbase.data_api.sequence.assembly.service import thrift_service
from doekbase.data_api.sequence.assembly.service.interface import \
AssemblyService
from doekbase.data_api.util import get_logger
_log = get_logger(__name__)
def start_service(**kw):
return service_core.start_service(AssemblyService, thrift_service, _log,
**kw)
stop_service = service_core.stop_service
__date__ = '9/30/15'
# System
import os
import threading
import time
import unittest
# Third-party
from dogpile.cache.api import NO_VALUE
# Local
from doekbase.data_api import cache
from doekbase.data_api import util
from doekbase.data_api.core import ObjectAPI
from . import shared
_log = util.get_logger(__name__)
# Uncomment this line to turn off DBM tests
USE_DBM = False
def setup():
shared.setup()
class TestCache(unittest.TestCase):
"""Test the cache.
"""
dbm_path = None
## Setup / teardown
# Third-party
from thrift.transport import TSocket
from thrift.transport import TTransport
from thrift.protocol import TJSONProtocol
from thrift.server import THttpServer
# Local
from doekbase.data_api.taxonomy.taxon.service import thrift_service
from doekbase.data_api.taxonomy.taxon.service.interface import TaxonService
from doekbase.data_api.util import get_logger
DEFAULT_WS_URL = 'https://ci.kbase.us/services/ws/'
DEFAULT_SHOCK_URL = 'https://ci.kbase.us/services/shock-api/'
_log = get_logger('thrift') # set up a logger for Thrift messages
_log.setLevel(logging.DEBUG)
def get_services_dict(ws=DEFAULT_WS_URL, shock=DEFAULT_SHOCK_URL):
return {'workspace_service_url': ws,
'shock_service_url': shock}
def taxon_service():
handler = TaxonService(services=get_services_dict())
processor = thrift_service.Processor(handler)
pfactory = TJSONProtocol.TJSONProtocolFactory()
server_address = ('127.0.0.1', 9090)
server = THttpServer.THttpServer(processor, server_address, pfactory)
return server
# Imports
# Stdlib
import json
import logging
import re
# Local
from doekbase.data_api.util import get_logger
from doekbase.data_api.util import log_start, log_end
from doekbase.data_api.util import get_auth_token
from . import thrift_service, ttypes
# Logging
_log = get_logger('object_api')
_log.setLevel(logging.DEBUG)
# Constants
NAMESPACE = 'Object'
REF_PATTERN = re.compile("(.+/.+(/[0-9].+)?)|(ws\.[1-9][0-9]+\.[1-9][0-9]+)")
# Classes and functions
class ObjectAPI(object):
"""API layer over the autogenerated Thrift interface.
This can handle both local and remote modes by use of alternate
implementations of the `client` parameter.
"""