def write(self, dbPath=None):
self.setName('ProjectSettings')
if dbPath is not None:
self.mapper = SqliteMapper(dbPath, globals())
else:
if self.mapper is None:
raise Exception("Can't write ProjectSettings without mapper or dbPath")
self.mapper.deleteAll()
self.mapper.insert(self)
self.mapper.commit()
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_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 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()
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 loadSettings(dbPath):
""" Load a ProjectSettings from dbPath. """
classDict = dict(globals())
classDict.update(pwobj.__dict__)
mapper = SqliteMapper(dbPath, classDict)
settingList = mapper.selectByClass('ProjectSettings')
n = len(settingList)
if n == 0:
raise Exception("Can't load ProjectSettings from %s" % dbPath)
elif n > 1:
raise Exception("Only one ProjectSettings is expected in db, found %d in %s" % (n, dbPath))
settings = settingList[0]
settings.mapper = mapper
return settings
def loadSettings(dbPath):
""" Load a ProjectSettings from dbPath. """
classDict = dict(globals())
classDict.update(pwobj.__dict__)
mapper = SqliteMapper(dbPath, classDict)
settingList = mapper.selectByClass('ProjectSettings')
n = len(settingList)
if n == 0:
raise Exception("Can't load ProjectSettings from %s" % dbPath)
elif n > 1:
raise Exception("Only one ProjectSettings is expected in db, found %d in %s" % (n, dbPath))
settings = settingList[0]
settings.mapper = mapper
return settings
class DbTreeProvider(ObjectTreeProvider):
"""Retrieve the elements from the database"""
def __init__(self, dbName, classesDict):
ObjectTreeProvider.__init__(self)
self.mapper = SqliteMapper(dbName, classesDict)
def _getObjectList(self):
return self.mapper.selectAll()
class DbTreeProvider(ObjectTreeProvider):
"""Retrieve the elements from the database"""
def __init__(self, dbName, classesDict):
ObjectTreeProvider.__init__(self)
self.mapper = SqliteMapper(dbName, classesDict)
def _getObjectList(self):
return self.mapper.selectAll()
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 = pwobj.Dict(default=pwprot.LegacyProtocol)
classesDict.update(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.
"""
#TODO: REMOVE THE USE OF globals() here
classesDict = dict(pwobj.__dict__)
classesDict.update(em.getProtocols())
classesDict.update(em.getObjects())
return SqliteMapper(sqliteFn, classesDict)
def write(self, dbPath=None):
self.setName('ProjectSettings')
if dbPath is not None:
self.mapper = SqliteMapper(dbPath, globals())
else:
if self.mapper is None:
raise Exception("Can't write ProjectSettings without mapper or dbPath")
self.mapper.deleteAll()
self.mapper.insert(self)
self.mapper.commit()
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()
def __init__(self, filename, dictClasses=None):
if dictClasses is None:
dictClasses = globals()
SqliteMapper.__init__(self, filename, dictClasses)
class ProjectSettings(pwobj.OrderedObject):
""" Store settings related to a project. """
COLOR_MODE_STATUS = 0
COLOR_MODE_LABELS = 1
COLOR_MODE_AGE = 2
COLOR_MODES = (COLOR_MODE_STATUS, COLOR_MODE_LABELS, COLOR_MODE_AGE)
def __init__(self, confs={}, **kwargs):
pwobj.OrderedObject.__init__(self, **kwargs)
self.config = ProjectConfig()
# Store the current view selected by the user
self.currentProtocolsView = pwobj.String()
# Store the color mode: 0= Status, 1=Labels, ...
self.colorMode = pwobj.Integer(ProjectSettings.COLOR_MODE_STATUS)
self.nodeList = NodeConfigList(
) # Store graph nodes positions and other info
self.labelsList = LabelsList() # Label list
self.mapper = None # This should be set when load, or write
self.runsView = pwobj.Integer(1) # by default the graph view
self.readOnly = pwobj.Boolean(False)
self.runSelection = pwobj.CsvList(int) # Store selected runs
self.dataSelection = pwobj.CsvList(int) # Store selected runs
# Some extra settings stored, now mainly used
# from the webtools
# Time when the project was created
self.creationTime = pwobj.String(dt.datetime.now())
# Number of days that this project is active
# if None, the project will not expire
# This is used in webtools where a limited time
# is allowed for each project
self.lifeTime = pwobj.Integer()
# Set a disk quota for the project (in Gb)
# if None, quota is unlimited
self.diskQuota = pwobj.Integer()
def commit(self):
""" Commit changes made. """
self.mapper.commit()
def getRunsView(self):
return self.runsView.get()
def setRunsView(self, value):
self.runsView.set(value)
def getReadOnly(self):
return self.readOnly.get()
def setReadOnly(self, value):
self.readOnly.set(value)
def getCreationTime(self):
return self.creationTime.datetime()
def setCreationTime(self, value):
self.creationTime.set(value)
def getLifeTime(self):
return self.lifeTime.get()
def setLifeTime(self, value):
self.lifeTime.set(value)
def getConfig(self):
return self.config
def getProtocolView(self):
return self.currentProtocolsView.get()
def setProtocolView(self, protocolView):
""" Set the new protocol Menu given its index.
The new ProtocolMenu will be returned.
"""
self.currentProtocolsView.set(protocolView)
def getColorMode(self):
return self.colorMode.get()
def setColorMode(self, colorMode):
""" Set the color mode to use when drawing the graph.
"""
self.colorMode.set(colorMode)
def statusColorMode(self):
return self.getColorMode() == self.COLOR_MODE_STATUS
def labelsColorMode(self):
return self.getColorMode() == self.COLOR_MODE_LABELS
def ageColorMode(self):
return self.getColorMode() == self.COLOR_MODE_AGE
def write(self, dbPath=None):
self.setName('ProjectSettings')
if dbPath is not None:
self.mapper = SqliteMapper(dbPath, globals())
else:
if self.mapper is None:
raise Exception(
"Can't write ProjectSettings without mapper or dbPath")
self.mapper.deleteAll()
self.mapper.insert(self)
self.mapper.commit()
def getNodes(self):
return self.nodeList
def getNodeById(self, nodeId):
return self.nodeList.getNode(nodeId)
def addNode(self, nodeId, **kwargs):
return self.nodeList.addNode(nodeId, **kwargs)
def getLabels(self):
return self.labelsList
@classmethod
def load(cls, dbPath):
""" Load a ProjectSettings from dbPath. """
classDict = dict(globals())
classDict.update(pwobj.__dict__)
mapper = SqliteMapper(dbPath, classDict)
settingList = mapper.selectByClass('ProjectSettings')
n = len(settingList)
if n == 0:
raise Exception("Can't load ProjectSettings from %s" % dbPath)
elif n > 1:
raise Exception(
"Only one ProjectSettings is expected in db, found %d in %s" %
(n, dbPath))
settings = settingList[0]
settings.mapper = mapper
return settings
def __init__(self, dbName, classesDict):
ObjectTreeProvider.__init__(self)
self.mapper = SqliteMapper(dbName, classesDict)
def __init__(self, dbName, classesDict):
ObjectTreeProvider.__init__(self)
self.mapper = SqliteMapper(dbName, classesDict)
class ProjectSettings(pwobj.OrderedObject):
""" Store settings related to a project. """
def __init__(self, confs={}, **kwargs):
pwobj.OrderedObject.__init__(self, **kwargs)
self.config = ProjectConfig()
self.currentProtocolsView = pwobj.String() # Store the current view selected by the user
self.nodeList = NodeConfigList() # Store graph nodes positions and other info
self.mapper = None # This should be set when load, or write
self.runsView = pwobj.Integer(1) # by default the graph view
self.readOnly = pwobj.Boolean(False)
self.runSelection = pwobj.CsvList(int) # Store selected runs
# Some extra settings stored, now mainly used
# from the webtools
self.creationTime = pwobj.String(dt.datetime.now()) # Time when the project was created
# Number of days that this project is active
# if None, the project will not expire
# This is used in webtools where a limited time
# is allowed for each project
self.lifeTime = pwobj.Integer()
# Set a disk quota for the project (in Gb)
# if None, quota is unlimited
self.diskQuota = pwobj.Integer()
def commit(self):
""" Commit changes made. """
self.mapper.commit()
def getRunsView(self):
return self.runsView.get()
def setRunsView(self, value):
self.runsView.set(value)
def getReadOnly(self):
return self.readOnly.get()
def setReadOnly(self, value):
self.readOnly.set(value)
def getCreationTime(self):
f = "%Y-%m-%d %H:%M:%S.%f"
creationTime = self.creationTime.get()
return dt.datetime.strptime(creationTime, f)
def setCreationTime(self, value):
self.creationTime.set(value)
def getLifeTime(self):
return self.lifeTime.get()
def setLifeTime(self, value):
self.lifeTime.set(value)
def getConfig(self):
return self.config
def getProtocolView(self):
return self.currentProtocolsView.get()
def setProtocolView(self, protocolView):
""" Set the new protocol Menu given its index.
The new ProtocolMenu will be returned.
"""
self.currentProtocolsView.set(protocolView)
def write(self, dbPath=None):
self.setName('ProjectSettings')
if dbPath is not None:
self.mapper = SqliteMapper(dbPath, globals())
else:
if self.mapper is None:
raise Exception("Can't write ProjectSettings without mapper or dbPath")
self.mapper.deleteAll()
self.mapper.insert(self)
self.mapper.commit()
def getNodes(self):
return self.nodeList
def getNodeById(self, nodeId):
return self.nodeList.getNode(nodeId)
def addNode(self, nodeId, **kwargs):
return self.nodeList.addNode(nodeId, **kwargs)
def __init__(self, filename, dictClasses=None):
if dictClasses is None:
dictClasses = globals()
SqliteMapper.__init__(self, filename, dictClasses)
class ProjectSettings(pwobj.OrderedObject):
""" Store settings related to a project. """
def __init__(self, confs={}, **kwargs):
pwobj.OrderedObject.__init__(self, **kwargs)
self.config = ProjectConfig()
self.currentProtocolsView = pwobj.String() # Store the current view selected by the user
self.nodeList = NodeConfigList() # Store graph nodes positions and other info
self.mapper = None # This should be set when load, or write
self.runsView = pwobj.Integer(1) # by default the graph view
self.readOnly = pwobj.Boolean(False)
self.runSelection = pwobj.CsvList(int) # Store selected runs
# Some extra settings stored, now mainly used
# from the webtools
self.creationTime = pwobj.String(dt.datetime.now()) # Time when the project was created
# Number of days that this project is active
# if None, the project will not expire
# This is used in webtools where a limited time
# is allowed for each project
self.lifeTime = pwobj.Integer()
# Set a disk quota for the project (in Gb)
# if None, quota is unlimited
self.diskQuota = pwobj.Integer()
def commit(self):
""" Commit changes made. """
self.mapper.commit()
def getRunsView(self):
return self.runsView.get()
def setRunsView(self, value):
self.runsView.set(value)
def getReadOnly(self):
return self.readOnly.get()
def setReadOnly(self, value):
self.readOnly.set(value)
def getCreationTime(self):
f = "%Y-%m-%d %H:%M:%S.%f"
creationTime = self.creationTime.get()
return dt.datetime.strptime(creationTime, f)
def setCreationTime(self, value):
self.creationTime.set(value)
def getLifeTime(self):
return self.lifeTime.get()
def setLifeTime(self, value):
self.lifeTime.set(value)
def getConfig(self):
return self.config
def getProtocolView(self):
return self.currentProtocolsView.get()
def setProtocolView(self, protocolView):
""" Set the new protocol Menu given its index.
The new ProtocolMenu will be returned.
"""
self.currentProtocolsView.set(protocolView)
def write(self, dbPath=None):
self.setName('ProjectSettings')
if dbPath is not None:
self.mapper = SqliteMapper(dbPath, globals())
else:
if self.mapper is None:
raise Exception("Can't write ProjectSettings without mapper or dbPath")
self.mapper.deleteAll()
self.mapper.insert(self)
self.mapper.commit()
def getNodes(self):
return self.nodeList
def getNodeById(self, nodeId):
return self.nodeList.getNode(nodeId)
def addNode(self, nodeId, **kwargs):
return self.nodeList.addNode(nodeId, **kwargs)