class Workflow(AbstractWorkflow):
def __init__(self, **kwargs):
"""
Initializes the Workflow super class, store the instance in the DB and in case
stores the starting parameters.
If initialized with an uuid the Workflow is loaded from the DB, if not a new
workflow is generated and added to the DB following the stack frameworks. This
means that only modules inside aiida.workflows are allowed to implements
the workflow super calls and be stored. The caller names, modules and files are
retrieved from the stack.
:param uuid: a string with the uuid of the object to be loaded.
:param params: a dictionary of storable objects to initialize the specific workflow
:raise: NotExistent: if there is no entry of the desired workflow kind with
the given uuid.
"""
from aiida.orm.backend import construct_backend
self._backend = construct_backend()
self._to_be_stored = True
self._logger = logger.getChild(self.__class__.__name__)
uuid = kwargs.pop('uuid', None)
if uuid is not None:
self._to_be_stored = False
if kwargs:
raise ValueError(
"If you pass a UUID, you cannot pass any further parameter"
)
self._dbworkflowinstance = DbWorkflow.query.filter_by(
uuid=uuid).first()
if not self._dbworkflowinstance:
raise NotExistent(
"No entry with the UUID {} found".format(uuid))
# self.logger.info("Workflow found in the database, now retrieved")
self._repo_folder = RepositoryFolder(section=self._section_name,
uuid=self.uuid)
else:
# ATTENTION: Do not move this code outside or encapsulate it in a function
stack = inspect.stack()
# cur_fr = inspect.currentframe()
# call_fr = inspect.getouterframes(cur_fr, 2)
# Get all the caller data
caller_frame = stack[1][0]
caller_file = stack[1][1]
caller_funct = stack[1][3]
caller_module = inspect.getmodule(caller_frame)
caller_module_class = caller_frame.f_locals.get('self',
None).__class__
if not caller_funct == "__init__":
raise SystemError(
"A workflow must implement the __init__ class explicitly")
# Test if the launcher is another workflow
# print "caller_module", caller_module
# print "caller_module_class", caller_module_class
# print "caller_file", caller_file
# print "caller_funct", caller_funct
# Accept only the aiida.workflows packages
if caller_module == None or not caller_module.__name__.startswith(
"aiida.workflows"):
raise SystemError("The superclass can't be called directly")
self.caller_module = caller_module.__name__
self.caller_module_class = caller_module_class.__name__
self.caller_file = caller_file
self.caller_funct = caller_funct
self._temp_folder = SandboxFolder()
self.current_folder.insert_path(self.caller_file,
self.caller_module_class)
# self.store()
# Test if there are parameters as input
params = kwargs.pop('params', None)
if params is not None:
if isinstance(params, dict):
self.set_params(params)
user = self._backend.users.get_automatic_user()
# This stores the MD5 as well, to test in case the workflow has
# been modified after the launch
self._dbworkflowinstance = DbWorkflow(
user=user.dbuser,
module=self.caller_module,
module_class=self.caller_module_class,
script_path=self.caller_file,
script_md5=md5_file(self.caller_file))
self.attach_calc_lazy_storage = {}
self.attach_subwf_lazy_storage = {}
@property
def dbworkflowinstance(self):
"""
Get the DbWorkflow object stored in the super class.
:return: DbWorkflow object from the database
"""
if self._dbworkflowinstance.id is None:
return self._dbworkflowinstance
else:
self._dbworkflowinstance = DbWorkflow.query.filter_by(
id=self._dbworkflowinstance.id).first()
return self._dbworkflowinstance
def _get_dbworkflowinstance(self):
return self.dbworkflowinstance
@property
def label(self):
"""
Get the label of the workflow.
:return: a string
"""
return self.dbworkflowinstance.label
@label.setter
def label(self, label):
self._update_db_label_field(label)
@property
def ctime(self):
return self.dbworkflowinstance.ctime
def _update_db_label_field(self, field_value):
"""
Safety method to store the label of the workflow
:return: a string
"""
self.dbworkflowinstance.label = field_value
if self.is_stored:
self._dbworkflowinstance.save(commit=False)
self._increment_version_number_db()
@property
def description(self):
"""
Get the description of the workflow.
:return: a string
"""
return self.dbworkflowinstance.description
@description.setter
def description(self, desc):
self._update_db_description_field(desc)
def _update_db_description_field(self, field_value):
"""
Safety method to store the description of the workflow
:return: a string
"""
self.dbworkflowinstance.description = field_value
if self.is_stored:
self._dbworkflowinstance.save(commit=False)
self._increment_version_number_db()
def _increment_version_number_db(self):
"""
This function increments the version number in the DB.
This should be called every time you need to increment the version (e.g. on adding a
extra or attribute).
"""
# I increment the node number using a filter (this should be the right way of doing it;
# dbnode.nodeversion = F('nodeversion') + 1
# will do weird stuff, returning Django Objects instead of numbers, and incrementing at
# every save; moreover in this way I should do the right thing for concurrent writings
session = sa.get_scoped_session()
self.dbworkflowinstance.nodeversion = DbWorkflow.nodeversion + 1
session.add(self.dbworkflowinstance)
session.commit()
@classmethod
def query(cls, *args, **kwargs):
"""
Map to the aiidaobjects manager of the DbWorkflow, that returns
Workflow objects instead of DbWorkflow entities.
"""
q = django_filter(DbWorkflow.aiida_query, **kwargs)
return q
@property
def logger(self):
"""
Get the logger of the Workflow object, so that it also logs to the
DB.
:return: LoggerAdapter object, that works like a logger, but also has
the 'extra' embedded
"""
return logging.LoggerAdapter(logger=self._logger,
extra=get_dblogger_extra(self))
def store(self):
"""
Stores the DbWorkflow object data in the database
"""
if not self.is_stored:
self._dbworkflowinstance.save()
if hasattr(self, '_params'):
self.dbworkflowinstance.add_parameters(self._params,
force=False)
self._repo_folder = \
RepositoryFolder(section=self._section_name, uuid=self.uuid)
self.repo_folder.replace_with_folder(
self.get_temp_folder().abspath, move=True, overwrite=True)
self._temp_folder = None
self._to_be_stored = False
# Important to allow to do w = WorkflowSubClass().store()
return self
@property
def uuid(self):
"""
Returns the DbWorkflow uuid
"""
return self.dbworkflowinstance.uuid
@property
def pk(self):
"""
Returns the DbWorkflow pk
"""
return self.dbworkflowinstance.id
def info(self):
"""
Returns an array with all the informations about the modules, file, class to locate
the workflow source code
"""
return [
self.dbworkflowinstance.module,
self.dbworkflowinstance.module_class,
self.dbworkflowinstance.script_path,
self.dbworkflowinstance.script_md5, self.dbworkflowinstance.ctime,
self.dbworkflowinstance.state
]
def set_params(self, params, force=False):
"""
Adds parameters to the Workflow that are both stored and used every time
the workflow engine re-initialize the specific workflow to launch the new methods.
"""
def par_validate(params):
the_params = {}
for k, v in params.iteritems():
if any([
isinstance(v, int),
isinstance(v, bool),
isinstance(v, float),
isinstance(v, str)
]):
the_params[k] = v
else:
raise ValidationError(
"Cannot store in the DB a parameter "
"which is not of type int, bool, float or str.")
return the_params
if not self.is_stored:
self._params = params
else:
the_params = par_validate(params)
self.dbworkflowinstance.add_parameters(the_params, force=force)
def get_parameters(self):
"""
Get the Workflow paramenters
:return: a dictionary of storable objects
"""
if not self.is_stored:
return self._params
else:
return self.dbworkflowinstance.get_parameters()
def get_parameter(self, _name):
"""
Get one Workflow paramenter
:param name: a string with the parameters name to retrieve
:return: a dictionary of storable objects
"""
if not self.is_stored:
return self._params(_name)
else:
return self.dbworkflowinstance.get_parameter(_name)
def get_attributes(self):
"""
Get the Workflow attributes
:return: a dictionary of storable objects
"""
return self.dbworkflowinstance.get_attributes()
def get_attribute(self, _name):
"""
Get one Workflow attribute
:param name: a string with the attribute name to retrieve
:return: a dictionary of storable objects
"""
return self.dbworkflowinstance.get_attribute(_name)
def add_attributes(self, _params):
"""
Add a set of attributes to the Workflow. If another attribute is present with the same name it will
be overwritten.
:param name: a string with the attribute name to store
:param value: a storable object to store
"""
if not self.is_stored:
raise ModificationNotAllowed(
"You cannot add attributes before storing")
self.dbworkflowinstance.add_attributes(_params)
def add_attribute(self, _name, _value):
"""
Add one attributes to the Workflow. If another attribute is present with the same name it will
be overwritten.
:param name: a string with the attribute name to store
:param value: a storable object to store
"""
if not self.is_stored:
raise ModificationNotAllowed(
"You cannot add attributes before storing")
self.dbworkflowinstance.add_attribute(_name, _value)
def get_results(self):
"""
Get the Workflow results
:return: a dictionary of storable objects
"""
return self.dbworkflowinstance.get_results()
def get_result(self, _name):
"""
Get one Workflow result
:param name: a string with the result name to retrieve
:return: a dictionary of storable objects
"""
return self.dbworkflowinstance.get_result(_name)
def add_results(self, _params):
"""
Add a set of results to the Workflow. If another result is present with the same name it will
be overwritten.
:param name: a string with the result name to store
:param value: a storable object to store
"""
self.dbworkflowinstance.add_results(_params)
def add_result(self, _name, _value):
"""
Add one result to the Workflow. If another result is present with the same name it will
be overwritten.
:param name: a string with the result name to store
:param value: a storable object to store
"""
self.dbworkflowinstance.add_result(_name, _value)
def get_state(self):
"""
Get the Workflow's state
:return: a state from wf_states in aiida.common.datastructures
"""
return unicode(self.dbworkflowinstance.state)
def set_state(self, state):
"""
Set the Workflow's state
:param name: a state from wf_states in aiida.common.datastructures
"""
self.dbworkflowinstance.set_state(state)
def is_new(self):
"""
Returns True is the Workflow's state is CREATED
"""
return self.dbworkflowinstance.state == wf_states.CREATED
def is_running(self):
"""
Returns True is the Workflow's state is RUNNING
"""
return self.dbworkflowinstance.state == wf_states.RUNNING
def has_finished_ok(self):
"""
Returns True is the Workflow's state is FINISHED
"""
return self.dbworkflowinstance.state in [
wf_states.FINISHED, wf_states.SLEEP
]
def has_failed(self):
"""
Returns True is the Workflow's state is ERROR
"""
return self.dbworkflowinstance.state == wf_states.ERROR
def is_subworkflow(self):
"""
Return True is this is a subworkflow (i.e., if it has a parent),
False otherwise.
"""
return self.dbworkflowinstance.is_subworkflow()
def get_step(self, step_method):
"""
Retrieves by name a step from the Workflow.
:param step_method: a string with the name of the step to retrieve or a method
:raise: ObjectDoesNotExist: if there is no step with the specific name.
:return: a DbWorkflowStep object.
"""
if isinstance(step_method, basestring):
step_method_name = step_method
else:
if not getattr(step_method, "is_wf_step"):
raise AiidaException(
"Cannot get step calculations from a method not decorated as Workflow method"
)
step_method_name = step_method.wf_step_name
if step_method_name == wf_exit_call:
raise InternalError(
"Cannot query a step with name {0}, reserved string".format(
step_method_name))
step_list = self.dbworkflowinstance.steps
automatic_user = self._backend.users.get_automatic_user()
step = [
_ for _ in step_list
if _.name == step_method_name and _.user == automatic_user.dbuser
]
try:
return step[0]
except IndexError:
return None
def get_steps(self, state=None):
"""
Retrieves all the steps from a specific workflow Workflow with the possibility to limit the list
to a specific step's state.
:param state: a state from wf_states in aiida.common.datastructures
:return: a list of DbWorkflowStep objects.
"""
step_list = self.dbworkflowinstance.steps
if state is not None:
step_list = [_ for _ in step_list if _.state == state]
steps_and_times = [[_.time, _] for _ in step_list]
steps_and_times = sorted(steps_and_times)
steps = [_[1] for _ in steps_and_times]
return steps
def get_report(self):
"""
Return the Workflow report.
:note: once, in case the workflow is a subworkflow of any other Workflow this method
calls the parent ``get_report`` method.
This is not the case anymore.
:return: a list of strings
"""
report = self.dbworkflowinstance.report or ''
return report.splitlines()
def clear_report(self):
"""
Wipe the Workflow report. In case the workflow is a subworflow of any other Workflow this method
calls the parent ``clear_report`` method.
"""
if len(self.dbworkflowinstance.parent_workflow_step.all()) == 0:
self.dbworkflowinstance.clear_report()
else:
Workflow(uuid=self.dbworkflowinstance.parent_workflow_step.first().
parent.uuid).clear_report()
def append_to_report(self, text):
"""
Adds text to the Workflow report.
:note: Once, in case the workflow is a subworkflow of any other Workflow this method
calls the parent ``append_to_report`` method; now instead this is not the
case anymore
"""
self.dbworkflowinstance.append_to_report(text)
@classmethod
def get_subclass_from_dbnode(cls, wf_db):
module = wf_db.module
module_class = wf_db.module_class
try:
wf_mod = importlib.import_module(module)
except ImportError:
raise InternalError(
"Unable to load the workflow module {}".format(module))
for elem_name in wf_mod.__dict__.iterkeys():
if module_class == elem_name: # and issubclass(elem, Workflow):
return getattr(wf_mod, elem_name)(uuid=wf_db.uuid)
@classmethod
def get_subclass_from_pk(cls, pk):
import aiida.backends.sqlalchemy
session = aiida.backends.sqlalchemy.get_scoped_session()
try:
session.begin_nested()
dbworkflowinstance = DbWorkflow.query.filter_by(id=pk).first()
except:
session.rollback()
raise
if not dbworkflowinstance:
raise NotExistent("No entry with pk= {} found".format(pk))
return cls.get_subclass_from_dbnode(dbworkflowinstance)
@classmethod
def get_subclass_from_uuid(cls, uuid):
import aiida.backends.sqlalchemy
session = aiida.backends.sqlalchemy.get_scoped_session()
try:
session.begin_nested()
dbworkflowinstance = DbWorkflow.query.filter_by(uuid=uuid).first()
except:
session.rollback()
raise
if not dbworkflowinstance:
raise NotExistent("No entry with the UUID {} found".format(uuid))
return cls.get_subclass_from_dbnode(dbworkflowinstance)
@classmethod
def step(cls, fun):
"""
This method is used as a decorator for workflow steps, and handles the method's execution,
the state updates and the eventual errors.
The decorator generates a wrapper around the input function to execute, adding with the correct
step name and a utility variable to make it distinguishable from non-step methods.
When a step is launched, the wrapper tries to run the function in case of error the state of
the workflow is moved to ERROR and the traceback is stored in the report. In general the input
method is a step obtained from the Workflow object, and the decorator simply handles a controlled
execution of the step allowing the code not to break in case of error in the step's source code.
The wrapper also tests not to run two times the same step, unless a Workflow is in ERROR state, in this
case all the calculations and subworkflows of the step are killed and a new execution is allowed.
:param fun: a methods to wrap, making it a Workflow step
:raise: AiidaException: in case the workflow state doesn't allow the execution
:return: the wrapped methods,
"""
import sys, traceback
wrapped_method = fun.__name__
# This function gets called only if the method is launched with the execution brackets ()
# Otherwise, when the method is addressed in a next() call this never gets called and only the
# attributes are added
def wrapper(self, *args, **kwargs):
# Store the workflow at the first step executed
if self._to_be_stored:
self.store()
if len(args) > 0:
raise AiidaException(
"A step method cannot have any argument, use add_attribute to the workflow"
)
# If a method is launched and the step is RUNNING or INITIALIZED we should stop
if self.has_step(wrapped_method) and \
not (self.get_step(wrapped_method).state == wf_states.ERROR or \
self.get_step(wrapped_method).state == wf_states.SLEEP or \
self.get_step(wrapped_method).nextcall == wf_default_call or \
self.get_step(wrapped_method).nextcall == wrapped_method \
# cls.has_step(wrapped_method) \
):
raise AiidaException(
"The step {0} has already been initialized, cannot change this outside the parent workflow !"
.format(wrapped_method))
# If a method is launched and the step is halted for ERROR, then clean the step and re-launch
if self.has_step(wrapped_method) and \
(self.get_step(wrapped_method).state == wf_states.ERROR or \
self.get_step(wrapped_method).state == wf_states.SLEEP):
for w in self.get_step(wrapped_method).get_sub_workflows():
w.kill()
self.get_step(wrapped_method).remove_sub_workflows()
for c in self.get_step(wrapped_method).get_calculations():
c.kill()
self.get_step(wrapped_method).remove_calculations()
# self.get_steps(wrapped_method).set_nextcall(wf_exit_call)
user = self._backend.users.get_automatic_user()
method_step, created = self.dbworkflowinstance._get_or_create_step(
name=wrapped_method, user=user.dbuser)
try:
fun(self)
except:
exc_type, exc_value, exc_traceback = sys.exc_info()
self.append_to_report(
"ERROR ! This workflow got an error in the {0} method, we report down the stack trace"
.format(wrapped_method))
self.append_to_report("full traceback: {0}".format(
traceback.format_exc()))
method_step.set_state(wf_states.ERROR)
self.set_state(wf_states.ERROR)
return None
out = wrapper
wrapper.is_wf_step = True
wrapper.wf_step_name = fun.__name__
return wrapper
def next(self, next_method):
"""
Adds the a new step to be called after the completion of the caller method's calculations and subworkflows.
This method must be called inside a Workflow step, otherwise an error is thrown. The
code finds the caller method and stores in the database the input next_method as the next
method to be called. At this point no execution in made, only configuration updates in the database.
If during the execution of the caller method the user launched calculations or subworkflows, this
method will add them to the database, making them available to the workflow manager to be launched.
In fact all the calculation and subworkflow submissions are lazy method, really executed by this call.
:param next_method: a Workflow step method to execute after the caller method
:raise: AiidaException: in case the caller method cannot be found or validated
:return: the wrapped methods, decorated with the correct step name
"""
md5 = self.dbworkflowinstance.script_md5
script_path = self.dbworkflowinstance.script_path
# TODO: in principles, the file containing the workflow description
# should be copied in a repository, and, on that file, the workflow
# should check to be sure of loading the same description of the
# workflow. At the moment, this is not done and is checking the source
# in aiida/workflows/... resulting essentially in the impossibility of
# developing a workflow without rendering most of the trial run
# unaccessible. I comment these lines for this moment.
# if md5 != md5_file(script_path):
# raise ValidationError("Unable to load the original workflow module from {}, MD5 has changed".format(script_path))
# ATTENTION: Do not move this code outside or encapsulate it in a function
curframe = inspect.currentframe()
calframe = inspect.getouterframes(curframe, 2)
caller_method = calframe[1][3]
if next_method is None:
raise AiidaException(
"The next method is None, probably you passed a method with parenthesis ??"
)
if not self.has_step(caller_method):
raise AiidaException(
"The caller method is either not a step or has not been registered as one"
)
if not next_method.__name__ == wf_exit_call:
try:
is_wf_step = getattr(next_method, "is_wf_step", None)
except AttributeError:
raise AiidaException(
"Cannot add as next call a method not decorated as Workflow method"
)
# TODO SP: abstract this, this depends on the DB. The better would be
# to add a method to the DbWorkflow from SQLA and Django to get steps
# with particular filters, in order to avoid repetition of all the code
# arround
automatic_user = self._backend.users.get_automatic_user()
# Retrieve the caller method
method_step, _ = self.dbworkflowinstance._get_or_create_step(
name=caller_method, user=automatic_user.dbuser)
# Attach calculations
if caller_method in self.attach_calc_lazy_storage:
for c in self.attach_calc_lazy_storage[caller_method]:
method_step.add_calculation(c)
# Attach sub-workflows
if caller_method in self.attach_subwf_lazy_storage:
for w in self.attach_subwf_lazy_storage[caller_method]:
method_step.add_sub_workflow(w)
# Set the next method
if not next_method.__name__ == wf_exit_call:
next_method_name = next_method.wf_step_name
else:
next_method_name = wf_exit_call
# logger.info("Adding step {0} after {1} in {2}".format(next_method_name, caller_method, self.uuid))
method_step.set_nextcall(next_method_name)
#
self.dbworkflowinstance.set_state(wf_states.RUNNING)
method_step.set_state(wf_states.RUNNING)
def __init__(self, **kwargs):
"""
Initializes the Workflow super class, store the instance in the DB and in case
stores the starting parameters.
If initialized with an uuid the Workflow is loaded from the DB, if not a new
workflow is generated and added to the DB following the stack frameworks. This
means that only modules inside aiida.workflows are allowed to implements
the workflow super calls and be stored. The caller names, modules and files are
retrieved from the stack.
:param uuid: a string with the uuid of the object to be loaded.
:param params: a dictionary of storable objects to initialize the specific workflow
:raise: NotExistent: if there is no entry of the desired workflow kind with
the given uuid.
"""
from aiida.orm.backend import construct_backend
self._backend = construct_backend()
self._to_be_stored = True
self._logger = logger.getChild(self.__class__.__name__)
uuid = kwargs.pop('uuid', None)
if uuid is not None:
self._to_be_stored = False
if kwargs:
raise ValueError(
"If you pass a UUID, you cannot pass any further parameter"
)
self._dbworkflowinstance = DbWorkflow.query.filter_by(
uuid=uuid).first()
if not self._dbworkflowinstance:
raise NotExistent(
"No entry with the UUID {} found".format(uuid))
# self.logger.info("Workflow found in the database, now retrieved")
self._repo_folder = RepositoryFolder(section=self._section_name,
uuid=self.uuid)
else:
# ATTENTION: Do not move this code outside or encapsulate it in a function
stack = inspect.stack()
# cur_fr = inspect.currentframe()
# call_fr = inspect.getouterframes(cur_fr, 2)
# Get all the caller data
caller_frame = stack[1][0]
caller_file = stack[1][1]
caller_funct = stack[1][3]
caller_module = inspect.getmodule(caller_frame)
caller_module_class = caller_frame.f_locals.get('self',
None).__class__
if not caller_funct == "__init__":
raise SystemError(
"A workflow must implement the __init__ class explicitly")
# Test if the launcher is another workflow
# print "caller_module", caller_module
# print "caller_module_class", caller_module_class
# print "caller_file", caller_file
# print "caller_funct", caller_funct
# Accept only the aiida.workflows packages
if caller_module == None or not caller_module.__name__.startswith(
"aiida.workflows"):
raise SystemError("The superclass can't be called directly")
self.caller_module = caller_module.__name__
self.caller_module_class = caller_module_class.__name__
self.caller_file = caller_file
self.caller_funct = caller_funct
self._temp_folder = SandboxFolder()
self.current_folder.insert_path(self.caller_file,
self.caller_module_class)
# self.store()
# Test if there are parameters as input
params = kwargs.pop('params', None)
if params is not None:
if isinstance(params, dict):
self.set_params(params)
user = self._backend.users.get_automatic_user()
# This stores the MD5 as well, to test in case the workflow has
# been modified after the launch
self._dbworkflowinstance = DbWorkflow(
user=user.dbuser,
module=self.caller_module,
module_class=self.caller_module_class,
script_path=self.caller_file,
script_md5=md5_file(self.caller_file))
self.attach_calc_lazy_storage = {}
self.attach_subwf_lazy_storage = {}
class Workflow(AbstractWorkflow):
def __init__(self, **kwargs):
"""
Initializes the Workflow super class, store the instance in the DB and in case
stores the starting parameters.
If initialized with an uuid the Workflow is loaded from the DB, if not a new
workflow is generated and added to the DB following the stack frameworks. This
means that only modules inside aiida.workflows are allowed to implements
the workflow super calls and be stored. The caller names, modules and files are
retrieved from the stack.
:param uuid: a string with the uuid of the object to be loaded.
:param params: a dictionary of storable objects to initialize the specific workflow
:raise: NotExistent: if there is no entry of the desired workflow kind with
the given uuid.
"""
self._to_be_stored = True
self._logger = logger.getChild(self.__class__.__name__)
uuid = kwargs.pop('uuid', None)
if uuid is not None:
self._to_be_stored = False
if kwargs:
raise ValueError("If you pass a UUID, you cannot pass any further parameter")
self._dbworkflowinstance = DbWorkflow.query.filter_by(uuid=uuid).first()
if not self._dbworkflowinstance:
raise NotExistent("No entry with the UUID {} found".format(uuid))
# self.logger.info("Workflow found in the database, now retrieved")
self._repo_folder = RepositoryFolder(section=self._section_name, uuid=self.uuid)
else:
# ATTENTION: Do not move this code outside or encapsulate it in a function
stack = inspect.stack()
# cur_fr = inspect.currentframe()
#call_fr = inspect.getouterframes(cur_fr, 2)
# Get all the caller data
caller_frame = stack[1][0]
caller_file = stack[1][1]
caller_funct = stack[1][3]
caller_module = inspect.getmodule(caller_frame)
caller_module_class = caller_frame.f_locals.get('self', None).__class__
if not caller_funct == "__init__":
raise SystemError("A workflow must implement the __init__ class explicitly")
# Test if the launcher is another workflow
# print "caller_module", caller_module
# print "caller_module_class", caller_module_class
# print "caller_file", caller_file
# print "caller_funct", caller_funct
# Accept only the aiida.workflows packages
if caller_module == None or not caller_module.__name__.startswith("aiida.workflows"):
raise SystemError("The superclass can't be called directly")
self.caller_module = caller_module.__name__
self.caller_module_class = caller_module_class.__name__
self.caller_file = caller_file
self.caller_funct = caller_funct
self._temp_folder = SandboxFolder()
self.current_folder.insert_path(self.caller_file, self.caller_module_class)
# self.store()
# Test if there are parameters as input
params = kwargs.pop('params', None)
if params is not None:
if isinstance(params, dict):
self.set_params(params)
# This stores the MD5 as well, to test in case the workflow has
# been modified after the launch
self._dbworkflowinstance = DbWorkflow(user=get_automatic_user(),
module=self.caller_module,
module_class=self.caller_module_class,
script_path=self.caller_file,
script_md5=md5_file(self.caller_file))
self.attach_calc_lazy_storage = {}
self.attach_subwf_lazy_storage = {}
@property
def dbworkflowinstance(self):
"""
Get the DbWorkflow object stored in the super class.
:return: DbWorkflow object from the database
"""
if self._dbworkflowinstance.id is None:
return self._dbworkflowinstance
else:
self._dbworkflowinstance = DbWorkflow.query.filter_by(id=self._dbworkflowinstance.id).first()
return self._dbworkflowinstance
def _get_dbworkflowinstance(self):
return self.dbworkflowinstance
@property
def label(self):
"""
Get the label of the workflow.
:return: a string
"""
return self.dbworkflowinstance.label
@label.setter
def label(self, label):
self._update_db_label_field(label)
def _update_db_label_field(self, field_value):
"""
Safety method to store the label of the workflow
:return: a string
"""
self.dbworkflowinstance.label = field_value
if not self._to_be_stored:
self._dbworkflowinstance.save(commit=False)
self._increment_version_number_db()
@property
def description(self):
"""
Get the description of the workflow.
:return: a string
"""
return self.dbworkflowinstance.description
@description.setter
def description(self, desc):
self._update_db_description_field(desc)
def _update_db_description_field(self, field_value):
"""
Safety method to store the description of the workflow
:return: a string
"""
self.dbworkflowinstance.description = field_value
if not self._to_be_stored:
self._dbworkflowinstance.save(commit=False)
self._increment_version_number_db()
def _increment_version_number_db(self):
"""
This function increments the version number in the DB.
This should be called every time you need to increment the version (e.g. on adding a
extra or attribute).
"""
# I increment the node number using a filter (this should be the right way of doing it;
# dbnode.nodeversion = F('nodeversion') + 1
# will do weird stuff, returning Django Objects instead of numbers, and incrementing at
# every save; moreover in this way I should do the right thing for concurrent writings
# I use self._dbnode because this will not do a query to update the node; here I only
# need to get its pk
self.dbworkflowinstance.nodeversion = DbWorkflow.nodeversion + 1
sa.session.add(self.dbworkflowinstance)
sa.session.commit()
@classmethod
def query(cls, *args, **kwargs):
"""
Map to the aiidaobjects manager of the DbWorkflow, that returns
Workflow objects instead of DbWorkflow entities.
"""
q = django_filter(DbWorkflow.aiida_query, **kwargs)
return q
@property
def logger(self):
"""
Get the logger of the Workflow object, so that it also logs to the
DB.
:return: LoggerAdapter object, that works like a logger, but also has
the 'extra' embedded
"""
return logging.LoggerAdapter(logger=self._logger,
extra=get_dblogger_extra(self))
def store(self):
"""
Stores the DbWorkflow object data in the database
"""
if self._to_be_stored:
self._dbworkflowinstance.save()
if hasattr(self, '_params'):
self.dbworkflowinstance.add_parameters(self._params, force=False)
self._repo_folder =\
RepositoryFolder(section=self._section_name, uuid=self.uuid)
self.repo_folder.replace_with_folder(
self.get_temp_folder().abspath, move=True, overwrite=True)
self._temp_folder = None
self._to_be_stored = False
# Important to allow to do w = WorkflowSubClass().store()
return self
@property
def uuid(self):
"""
Returns the DbWorkflow uuid
"""
return self.dbworkflowinstance.uuid
@property
def pk(self):
"""
Returns the DbWorkflow pk
"""
return self.dbworkflowinstance.id
def info(self):
"""
Returns an array with all the informations about the modules, file, class to locate
the workflow source code
"""
return [self.dbworkflowinstance.module,
self.dbworkflowinstance.module_class,
self.dbworkflowinstance.script_path,
self.dbworkflowinstance.script_md5,
self.dbworkflowinstance.ctime,
self.dbworkflowinstance.state]
def set_params(self, params, force=False):
"""
Adds parameters to the Workflow that are both stored and used every time
the workflow engine re-initialize the specific workflow to launch the new methods.
"""
def par_validate(params):
the_params = {}
for k, v in params.iteritems():
if any([isinstance(v, int),
isinstance(v, bool),
isinstance(v, float),
isinstance(v, str)]):
the_params[k] = v
else:
raise ValidationError("Cannot store in the DB a parameter "
"which is not of type int, bool, float or str.")
return the_params
if self._to_be_stored:
self._params = params
else:
the_params = par_validate(params)
self.dbworkflowinstance.add_parameters(the_params, force=force)
def get_parameters(self):
"""
Get the Workflow paramenters
:return: a dictionary of storable objects
"""
if self._to_be_stored:
return self._params
else:
return self.dbworkflowinstance.get_parameters()
def get_parameter(self, _name):
"""
Get one Workflow paramenter
:param name: a string with the parameters name to retrieve
:return: a dictionary of storable objects
"""
if self._to_be_stored:
return self._params(_name)
else:
return self.dbworkflowinstance.get_parameter(_name)
def get_attributes(self):
"""
Get the Workflow attributes
:return: a dictionary of storable objects
"""
return self.dbworkflowinstance.get_attributes()
def get_attribute(self, _name):
"""
Get one Workflow attribute
:param name: a string with the attribute name to retrieve
:return: a dictionary of storable objects
"""
return self.dbworkflowinstance.get_attribute(_name)
def add_attributes(self, _params):
"""
Add a set of attributes to the Workflow. If another attribute is present with the same name it will
be overwritten.
:param name: a string with the attribute name to store
:param value: a storable object to store
"""
if self._to_be_stored:
raise ModificationNotAllowed("You cannot add attributes before storing")
self.dbworkflowinstance.add_attributes(_params)
def add_attribute(self, _name, _value):
"""
Add one attributes to the Workflow. If another attribute is present with the same name it will
be overwritten.
:param name: a string with the attribute name to store
:param value: a storable object to store
"""
if self._to_be_stored:
raise ModificationNotAllowed("You cannot add attributes before storing")
self.dbworkflowinstance.add_attribute(_name, _value)
def get_results(self):
"""
Get the Workflow results
:return: a dictionary of storable objects
"""
return self.dbworkflowinstance.get_results()
def get_result(self, _name):
"""
Get one Workflow result
:param name: a string with the result name to retrieve
:return: a dictionary of storable objects
"""
return self.dbworkflowinstance.get_result(_name)
def add_results(self, _params):
"""
Add a set of results to the Workflow. If another result is present with the same name it will
be overwritten.
:param name: a string with the result name to store
:param value: a storable object to store
"""
self.dbworkflowinstance.add_results(_params)
def add_result(self, _name, _value):
"""
Add one result to the Workflow. If another result is present with the same name it will
be overwritten.
:param name: a string with the result name to store
:param value: a storable object to store
"""
self.dbworkflowinstance.add_result(_name, _value)
def get_state(self):
"""
Get the Workflow's state
:return: a state from wf_states in aiida.common.datastructures
"""
return self.dbworkflowinstance.state
def set_state(self, state):
"""
Set the Workflow's state
:param name: a state from wf_states in aiida.common.datastructures
"""
self.dbworkflowinstance.set_state(state)
def is_new(self):
"""
Returns True is the Workflow's state is CREATED
"""
return self.dbworkflowinstance.state == wf_states.CREATED
def is_running(self):
"""
Returns True is the Workflow's state is RUNNING
"""
return self.dbworkflowinstance.state == wf_states.RUNNING
def has_finished_ok(self):
"""
Returns True is the Workflow's state is FINISHED
"""
return self.dbworkflowinstance.state in [wf_states.FINISHED, wf_states.SLEEP]
def has_failed(self):
"""
Returns True is the Workflow's state is ERROR
"""
return self.dbworkflowinstance.state == wf_states.ERROR
def is_subworkflow(self):
"""
Return True is this is a subworkflow (i.e., if it has a parent),
False otherwise.
"""
return self.dbworkflowinstance.is_subworkflow()
def get_step(self, step_method):
"""
Retrieves by name a step from the Workflow.
:param step_method: a string with the name of the step to retrieve or a method
:raise: ObjectDoesNotExist: if there is no step with the specific name.
:return: a DbWorkflowStep object.
"""
if isinstance(step_method, basestring):
step_method_name = step_method
else:
if not getattr(step_method, "is_wf_step"):
raise AiidaException("Cannot get step calculations from a method not decorated as Workflow method")
step_method_name = step_method.wf_step_name
if step_method_name == wf_exit_call:
raise InternalError("Cannot query a step with name {0}, reserved string".format(step_method_name))
step = self.dbworkflowinstance.steps.filter_by(name=step_method_name, user=get_automatic_user()).first()
return step
def get_steps(self, state=None):
"""
Retrieves all the steps from a specific workflow Workflow with the possibility to limit the list
to a specific step's state.
:param state: a state from wf_states in aiida.common.datastructures
:return: a list of DbWorkflowStep objects.
"""
if state is None:
return self.dbworkflowinstance.steps.order_by('time').all()
else:
return self.dbworkflowinstance.steps.filter_by(state=state).order_by('time').all()
def get_report(self):
"""
Return the Workflow report.
:note: once, in case the workflow is a subworkflow of any other Workflow this method
calls the parent ``get_report`` method.
This is not the case anymore.
:return: a list of strings
"""
return self.dbworkflowinstance.report.splitlines()
def clear_report(self):
"""
Wipe the Workflow report. In case the workflow is a subworflow of any other Workflow this method
calls the parent ``clear_report`` method.
"""
if len(self.dbworkflowinstance.parent_workflow_step.all()) == 0:
self.dbworkflowinstance.clear_report()
else:
Workflow(uuid=self.dbworkflowinstance.parent_workflow_step.first().parent.uuid).clear_report()
def append_to_report(self, text):
"""
Adds text to the Workflow report.
:note: Once, in case the workflow is a subworkflow of any other Workflow this method
calls the parent ``append_to_report`` method; now instead this is not the
case anymore
"""
self.dbworkflowinstance.append_to_report(text)
@classmethod
def get_subclass_from_dbnode(cls, wf_db):
module = wf_db.module
module_class = wf_db.module_class
try:
wf_mod = importlib.import_module(module)
except ImportError:
raise InternalError("Unable to load the workflow module {}".format(module))
for elem_name in wf_mod.__dict__.iterkeys():
if module_class == elem_name: #and issubclass(elem, Workflow):
return getattr(wf_mod, elem_name)(uuid=wf_db.uuid)
@classmethod
def get_subclass_from_pk(cls, pk):
dbworkflowinstance = DbWorkflow.query.filter_by(pk=pk).first()
if not dbworkflowinstance:
raise NotExistent("No entry with pk= {} found".format(pk))
return cls.get_subclass_from_dbnode(dbworkflowinstance)
@classmethod
def get_subclass_from_uuid(cls, uuid):
dbworkflowinstance = DbWorkflow.query.filter_by(uuid=uuid).first()
if not dbworkflowinstance:
raise NotExistent("No entry with the UUID {} found".format(uuid))
return cls.get_subclass_from_dbnode(dbworkflowinstance)