def test_init_no_rdf_store(self):
""" Should be able to init without these values """
c = Configure()
Configureable.default = c
d = Data()
try:
d.openDatabase()
except Exception:
self.fail("Bad state")
def test_namespace_manager(self):
c = Configure()
c['rdf.source'] = 'default'
c['rdf.store'] = 'default'
Configureable.default = c
d = Data()
d.openDatabase()
self.assertIsInstance(d['rdf.namespace_manager'], R.namespace.NamespaceManager)
def test_read_from_file_success(self):
""" Read configuration from a JSON file """
try:
d = Data.open("tests/test.conf")
self.assertEqual("test_value", d["test_variable"])
except Exception:
self.fail("test.conf should exist and be valid JSON")
def test_read_from_file_success(self):
""" Read configuration from a JSON file """
try:
d = Data.open("tests/test.conf")
self.assertEqual("test_value", d["test_variable"])
except Exception:
self.fail("test.conf should exist and be valid JSON")
def _conf(self):
from PyOpenWorm.data import Data
dat = getattr(self, '_dat', None)
if not dat or self._dat_file != self.config_file:
dat = Data.open(self.config_file)
stored_conf = dat.get('rdf.store_conf', None)
if stored_conf and not isabs(stored_conf):
dat['rdf.store_conf'] = abspath(pth_join(self.basedir, stored_conf))
dat.init_database()
self._dat = dat
self._dat_file = self.config_file
return dat
def test_ZODB_persistence(self):
""" Should be able to init without these values """
c = Configure()
fname = 'ZODB.fs'
c['rdf.source'] = 'ZODB'
c['rdf.store_conf'] = fname
Configureable.default = c
d = Data()
try:
d.openDatabase()
g = make_graph(20)
for x in g:
d['rdf.graph'].add(x)
d.closeDatabase()
d.openDatabase()
self.assertEqual(20, len(list(d['rdf.graph'])))
d.closeDatabase()
except Exception:
traceback.print_exc()
self.fail("Bad state")
delete_zodb_data_store(fname)
def _conf(self):
from PyOpenWorm.data import Data
dat = getattr(self, '_dat', None)
if not dat or self._dat_file != self.config_file:
dat = Data.open(self.config_file)
stored_conf = dat.get('rdf.store_conf', None)
if stored_conf and not isabs(stored_conf):
dat['rdf.store_conf'] = abspath(
pth_join(self.basedir, stored_conf))
dat.init_database()
self._dat = dat
self._dat_file = self.config_file
return dat
def test_Sleepycat_persistence(self):
""" Should be able to init without these values """
c = Configure()
fname = 'Sleepycat_store'
c['rdf.source'] = 'Sleepycat'
c['rdf.store_conf'] = fname
Configureable.default = c
d = Data()
try:
d.openDatabase()
g = make_graph(20)
for x in g:
d['rdf.graph'].add(x)
d.closeDatabase()
d.openDatabase()
self.assertEqual(20, len(list(d['rdf.graph'])))
d.closeDatabase()
except Exception:
traceback.print_exc()
self.fail("Bad state")
subprocess.call("rm -rf "+fname, shell=True)
def setUp(self):
# Set do_logging to True if you like walls of text
self.TestConfig = Data.open(TEST_CONFIG)
td = '__tempdir__'
z = self.TestConfig['rdf.store_conf']
if z.startswith(td):
x = z[len(td):]
h = tempfile.mkdtemp()
self.TestConfig['rdf.store_conf'] = h + x
self.delete_dir()
self.connection = PyOpenWorm.connect(conf=self.TestConfig, do_logging=False)
self.context = Context(ident='http://example.org/test-context',
conf=self.TestConfig)
typ = type(self)
if hasattr(typ, 'ctx_classes'):
if isinstance(dict, typ.ctx_classes):
self.ctx = self.context(typ.ctx_classes)
else:
self.ctx = self.context({x.__name__: x for x in typ.ctx_classes})
See: "Metadata in PyOpenWorm" for discussion on semantics of what giving
evidence for an object means.
"""
from __future__ import absolute_import
from __future__ import print_function
import PyOpenWorm as P
from PyOpenWorm.evidence import Evidence
from PyOpenWorm.neuron import Neuron
from PyOpenWorm.document import Document
from PyOpenWorm.data import Data
from PyOpenWorm.context import Context
# Create dummy database configuration.
d = Data()
# Connect to database with dummy configuration
conn = P.connect(conf=d)
ctx = Context(ident='http://example.org/data', conf=conn.conf)
evctx = Context(ident='http://example.org/meta', conf=conn.conf)
# Create a new Neuron object to work with
n = ctx(Neuron)(name='AVAL')
# Create a new Evidence object with `doi` and `pmid` fields populated.
# See `PyOpenWorm/evidence.py` for other available fields.
d = evctx(Document)(key='Anonymous2011',
doi='125.41.3/ploscompbiol',
pmid='12345678')
def test_read_from_file_fail(self):
""" Fail on attempt to read configuration from a non-JSON file """
with self.assertRaises(ValueError):
Data.open("tests/test_data/bad_test.conf")
def test_read_from_file_fail(self):
""" Fail on attempt to read configuration from a non-JSON file """
with self.assertRaises(ValueError):
Data.open("tests/test_data/bad_test.conf")
See: "Metadata in PyOpenWorm" for discussion on semantics of what giving
evidence for an object means.
"""
from __future__ import absolute_import
from __future__ import print_function
import PyOpenWorm as P
from PyOpenWorm.evidence import Evidence
from PyOpenWorm.neuron import Neuron
from PyOpenWorm.document import Document
from PyOpenWorm.data import Data
from PyOpenWorm.context import Context
# Create dummy database configuration.
d = Data({'rdf.source': 'ZODB'})
# Connect to database with dummy configuration
P.connect(conf=d)
ctx = Context(ident='http://example.org/data')
evctx = Context(ident='http://example.org/meta')
# Create a new Neuron object to work with
n = ctx(Neuron)(name='AVAL')
# Create a new Evidence object with `doi` and `pmid` fields populated.
# See `PyOpenWorm/evidence.py` for other available fields.
d = evctx(Document)(key='Anonymous2011',
doi='125.41.3/ploscompbiol',
pmid='12345678')
