def test_StepExecutor(self):
"""Test the list with several Complex"""
fn = self.getOutputPath("protocol.sqlite")
mapper = SqliteMapper(fn, globals())
prot = MyProtocol(mapper=mapper,
n=2,
workingDir=self.getOutputPath(''))
prot._stepsExecutor = StepExecutor(hostConfig=None)
prot.run()
self.assertEqual(prot._steps[0].getStatus(), STATUS_FINISHED)
mapper2 = SqliteMapper(fn, globals())
prot2 = mapper2.selectById(prot.getObjId())
self.assertEqual(prot.endTime.get(), prot2.endTime.get())
def createMapper(self, sqliteFn):
""" Create a new SqliteMapper object and pass as classes dict
all globas and update with data and protocols from em.
"""
#TODO: REMOVE THE USE OF globals() here
classesDict = dict(pwobj.__dict__)
classesDict.update(em.getProtocols())
classesDict.update(em.getObjects())
return SqliteMapper(sqliteFn, classesDict)
def createMapper(self, sqliteFn):
""" Create a new SqliteMapper object and pass as classes dict
all globas and update with data and protocols from em.
"""
classesDict = dict(pwobj.__dict__)
classesDict.update(em.getProtocols())
classesDict.update(em.getObjects())
mapper = SqliteMapper(sqliteFn, classesDict)
if not self.chdir:
mapper.setWorkingDir(self.path)
return mapper
def test_basicObjectOutput(self):
"""Test the list with several Complex"""
fn = self.getOutputPath("protocol.sqlite")
mapper = SqliteMapper(fn, globals())
prot = ProtOutputTest(mapper=mapper,
n=2,
workingDir=self.getOutputPath(''))
# Add and old style output, not in the outputs dictionary
prot.output1 = EMObject()
self.assertFalse(prot._useOutputList.get(),
"useOutputList wrongly initialized")
outputs = [output for output in prot.iterOutputAttributes()]
self.assertTrue(1, len(outputs))
prot._stepsExecutor = StepExecutor(hostConfig=None)
prot.run()
self.assertEqual(prot._steps[0].getStatus(), STATUS_FINISHED)
# Check there is an output
self.assertOutput(prot)
outputs = [output for output in prot.iterOutputAttributes()]
# We are intentionally ignoring a protocol with output (EMObject)
# That has been continued, We do not find a real case now.
self.assertEqual(1,
len(outputs),
msg="Integer output not registered properly.")
outputs = [output for output in prot.iterOutputAttributes(Integer)]
# Test passing a filter
self.assertEqual(1,
len(outputs),
msg="Integer not matched when filtering outputs.")
# Test with non existing class
outputs = [output for output in prot.iterOutputAttributes(DataSet)]
# Test passing a class
self.assertEqual(0,
len(outputs),
msg="Filter by class in iterOutputAttributes does "
"not work.")
self.assertTrue(prot._useOutputList.get(),
"useOutputList not activated")
def saveConfig(filename):
from pyworkflow.mapper import SqliteMapper
from pyworkflow.object import String, Integer
mapper = SqliteMapper(filename)
o = Config()
for k, v in globals().iteritems():
if k.startswith('cfg'):
if type(v) is str:
value = String(v)
else:
value = Integer(v)
setattr(o, k, value)
mapper.insert(o)
mapper.commit()
