def __init__(self, name=None, project=None, filename=None, folder=None):
if name is None: name = 'Default'
self.projectref = sc.Link(project) # Store pointer for the project
self.name = sc.uniquename(
name, namelist=self.projectref().burdensets.keys(
)) # Name of the parameter set, e.g. 'default'
self.uid = sc.uuid() # ID
self.created = sc.now() # Date created
self.modified = sc.now() # Date modified
# Define hard-coded column names
self.colnames = sc.odict([
('active', 'Active'),
#('code', 'Code'),
('cause', 'Cause'),
('dalys', 'DALYs'),
('deaths', 'Deaths'),
('prevalence', 'Prevalence')
])
# Load data, if provided
self.data = None
if filename is not None:
self.loaddata(filename=filename, folder=folder)
return None
def launch_task(task_id='', func_name='', args=[], kwargs={}):
match_taskrec = datastore.loadtask(task_id) # Find a matching task record (if any) to the task_id.
if match_taskrec is None: # If we did not find a match...
if not func_name in task_func_dict: # If the function name is not in the task function dictionary, return an error.
return_dict = {'error': 'Could not find requested async task function "%s"' % func_name}
else:
new_task_record = Task(task_id) # Create a new TaskRecord.
# Initialize the TaskRecord with available information.
new_task_record.status = 'queued'
new_task_record.queue_time = sc.now()
new_task_record.func_name = func_name
new_task_record.args = args
new_task_record.kwargs = kwargs
datastore.savetask(new_task_record) # Add the TaskRecord to the TaskDict.
# Queue up run_task() for Celery.
my_result = run_task.delay(task_id, func_name, args, kwargs)
new_task_record.result_id = my_result.id # Add the result ID to the TaskRecord, and update the DataStore.
datastore.savetask(new_task_record)
return_dict = new_task_record.jsonify() # Create the return dict from the user repr.
else: # Otherwise (there is a matching task)...
if match_taskrec.status == 'completed' or match_taskrec.status == 'error': # If the TaskRecord indicates the task has been completed or thrown an error...
if match_taskrec.result_id is not None: # If we have a result ID, erase the result from Redis.
result = celery_instance.AsyncResult(match_taskrec.result_id)
result.forget()
match_taskrec.result_id = None
# Initialize the TaskRecord to start the task again (though possibly with a new function and arguments).
match_taskrec.status = 'queued'
match_taskrec.queue_time = sc.now()
match_taskrec.start_time = None
match_taskrec.stop_time = None
match_taskrec.pending_time = None
match_taskrec.execution_time = None
match_taskrec.func_name = func_name
match_taskrec.args = args
match_taskrec.kwargs = kwargs
# Queue up run_task() for Celery.
my_result = run_task.delay(task_id, func_name, args, kwargs)
match_taskrec.result_id = my_result.id # Add the new result ID to the TaskRecord, and update the DataStore.
datastore.savetask(match_taskrec)
return_dict = match_taskrec.jsonify() # Create the return dict from the user repr.
else: # Else (the task is not completed)...
return_dict = {'error': 'Task is already %s' % match_taskrec.status}
return return_dict # Return our result.
def set_metadata(self, filename):
''' Set the metadata for the simulation -- creation time and filename '''
self.created = sc.now()
if filename is None:
datestr = sc.getdate(obj=self.created, dateformat='%Y-%b-%d_%H.%M.%S')
self.filename = f'covasim_{datestr}.sim'
return
def __init__(self,
sim=None,
metapars=None,
scenarios=None,
basepars=None,
filename=None):
# For this object, metapars are the foundation
default_pars = make_metapars() # Start with default pars
super().__init__(
default_pars) # Initialize and set the parameters as attributes
# Handle filename
self.created = sc.now()
if filename is None:
datestr = sc.getdate(obj=self.created,
dateformat='%Y-%b-%d_%H.%M.%S')
filename = f'covasim_scenarios_{datestr}.scens'
self.filename = filename
# Handle scenarios -- by default, create a baseline scenario
if scenarios is None:
scenarios = sc.dcp(default_scenario)
self.scenarios = scenarios
# Handle metapars
if metapars is None:
metapars = {}
self.metapars = metapars
self.update_pars(self.metapars)
# Create the simulation and handle basepars
if sim is None:
sim = cvsim.Sim()
self.base_sim = sim
if basepars is None:
basepars = {}
self.basepars = basepars
self.base_sim.update_pars(self.basepars)
self.base_sim.validate_pars()
self.base_sim.init_results()
# Copy quantities from the base sim to the main object
self.npts = self.base_sim.npts
self.tvec = self.base_sim.tvec
self.reskeys = self.base_sim.reskeys
# Create the results object; order is: results key, scenario, best/low/high
self.sims = sc.objdict()
self.allres = sc.objdict()
for reskey in self.reskeys:
self.allres[reskey] = sc.objdict()
for scenkey in scenarios.keys():
self.allres[reskey][scenkey] = sc.objdict()
for nblh in ['name', 'best', 'low', 'high']:
self.allres[reskey][scenkey][
nblh] = None # This will get populated below
return
def set_metadata(self, simfile, label):
''' Set the metadata for the simulation -- creation time and filename '''
self.created = sc.now()
self.version = cvv.__version__
self.git_info = cvm.git_info()
if simfile is None:
datestr = sc.getdate(obj=self.created, dateformat='%Y-%b-%d_%H.%M.%S')
self.simfile = f'covasim_{datestr}.sim'
if label is not None:
self.label = label
return
def check_task(task_id, verbose=False):
match_taskrec = datastore.loadtask(task_id) # Find a matching task record (if any) to the task_id.
if match_taskrec is None: # Check to see if the task exists, and if not, return an error.
errormsg = {'error': 'No task found for specified task ID (%s)' % task_id}
if verbose: print(errormsg)
return errormsg
else: # Update the elapsed times.
if match_taskrec.pending_time is not None: # If we are no longer pending...
pending_time = match_taskrec.pending_time # Use the existing pending_time.
if match_taskrec.execution_time is not None: # If we have finished executing...
execution_time = match_taskrec.execution_time # Use the execution time in the record.
else: # Else (we are still executing)...
execution_time = (sc.now() - match_taskrec.start_time).total_seconds()
else: # Else (we are still pending)...
pending_time = (sc.now() - match_taskrec.queue_time).total_seconds()
execution_time = 0
taskrec_dict = match_taskrec.jsonify() # Create the return dict from the user repr.
taskrec_dict['pendingTime'] = pending_time
taskrec_dict['executionTime'] = execution_time
if verbose: sc.pp(taskrec_dict)
return taskrec_dict # Return the has record information and elapsed times.
def __init__(self,
project=None,
name=None,
burdenset=None,
intervset=None,
makepackage=None):
self.name = name # Name of the parameter set, e.g. 'default'
self.uid = sc.uuid() # ID
self.projectref = sc.Link(
project) # Store pointer for the project, if available
self.created = sc.now() # Date created
self.modified = sc.now() # Date modified
self.eps = 1e-4 # A nonzero value to help with division
self.burdenset = burdenset
self.intervset = intervset
self.budget = None
self.frpwt = None
self.equitywt = None
self.data = None # The data
if makepackage: self.makepackage()
return None
def __init__(self,
name='Default',
burdenfile=None,
interventionsfile=None,
country=None,
makepackage=True,
verbose=2):
''' Initialize the project '''
## Define the structure sets
self.burdensets = sc.odict()
self.intervsets = sc.odict()
self.packagesets = sc.odict()
## Define other quantities
self.name = name
self.country = country
self.uid = sc.uuid()
self.created = sc.now()
self.modified = sc.now()
self.version = hp.version
self.gitinfo = sc.gitinfo(__file__)
self.filename = None # File path, only present if self.save() is used
## Load burden spreadsheet, if available
if burdenfile:
self.loadburden(filename=burdenfile, verbose=verbose)
## Load interventions spreadsheet, if available
if interventionsfile:
self.loadinterventions(filename=interventionsfile, verbose=verbose)
## Combine into health package, if available
if makepackage and burdenfile and interventionsfile:
self.makepackage()
return None
def __init__(self, name=None, project=None, filename=None, folder=None):
if name is None: name = 'Default'
self.projectref = sc.Link(project) # Store pointer for the project
self.name = sc.uniquename(name, namelist=self.projectref().intervsets.keys()) # Name of the parameter set, e.g. 'default'
self.uid = sc.uuid() # ID
self.created = sc.now() # Date created
self.modified = sc.now() # Date modified
# Define hard-coded column names
self.colnames = sc.odict([('active', 'Active'),
('shortname','Short name'),
('platform', 'Platform'),
('burdencov','Causes of burden (max coverage)'),
('icer', 'ICER'),
('unitcost', 'Unit cost'),
('spend', 'Spending'),
('frp', 'FRP'),
('equity', 'Equity'),
])
self.data = None
if filename is not None:
self.loaddata(filename=filename, folder=folder)
return None
def __init__(self, obj=None, key=None, objtype=None, uid=None, force=True):
# Handle input arguments
if uid is None:
if force:
uid = sc.uuid()
else:
errormsg = 'DataStore: Not creating a new Blob UUID since force is set to False: key=%s, objtype=%s, uid=%s, obj=%s' % (
key, objtype, uid, obj)
raise Exception(errormsg)
if not key: key = '%s%s%s' % (objtype, default_separator, uid)
# Set attributes
self.key = key
self.objtype = objtype
self.uid = uid
self.created = sc.now()
self.modified = [self.created]
self.obj = obj
return None
def __init__(self, pars=None, datafile=None, filename=None):
default_pars = cvpars.make_pars() # Start with default pars
super().__init__(
default_pars) # Initialize and set the parameters as attributes
self.datafile = datafile # Store this
self.data = None
if datafile is not None: # If a data file is provided, load it
self.data = cvpars.load_data(datafile)
self.created = sc.now()
if filename is None:
datestr = sc.getdate(obj=self.created,
dateformat='%Y-%b-%d_%H.%M.%S')
filename = f'covasim_{datestr}.sim'
self.filename = filename
self.stopped = None # If the simulation has stopped
self.results_ready = False # Whether or not results are ready
self.people = {}
self.results = {}
self.calculated = {}
if pars is not None:
self.update_pars(pars)
return
def get_fn():
''' Get a filename from the date '''
string = sc.sanitizefilename(str(sc.now())).replace(' ', '_')
return string
def save_project(project, die=None): # NB, only for saving an existing project
project.modified = sc.now()
output = datastore.saveblob(obj=project, objtype='project', die=die)
return output
def set_metadata(obj):
''' Set standard metadata for an object '''
obj.version = spv.__version__
obj.created = sc.now()
obj.git_info = sc.gitinfo(__file__, verbose=False)
return
def update(self):
''' When the object is updated, append the current time to the modified list '''
now = sc.now()
self.modified.append(now)
return now
def _do_RPC(self, verbose=False):
# Check to see whether the RPC is getting passed in in request.form.
# If so, we are doing an upload, and we want to download the RPC
# request info from the form, not request.data.
if 'funcname' in request.form: # Pull out the function name, args, and kwargs
fn_name = request.form.get('funcname')
try:
args = json.loads(request.form.get('args', "[]"),
object_pairs_hook=OrderedDict)
except:
args = [] # May or may not be present
try:
kwargs = json.loads(request.form.get('kwargs', "{}"),
object_pairs_hook=OrderedDict)
except:
kwargs = {} # May or may not be present
else: # Otherwise, we have a normal or download RPC, which means we pull the RPC request info from request.data.
reqdict = json.loads(request.data, object_pairs_hook=OrderedDict)
fn_name = reqdict['funcname']
args = reqdict.get('args', [])
kwargs = reqdict.get('kwargs', {})
if verbose:
print('RPC(): RPC properties:')
print(' fn_name: %s' % fn_name)
print(' args: %s' % args)
print(' kwargs: %s' % kwargs)
# If the function name is not in the RPC dictionary, return an error.
if not sc.isstring(fn_name):
return robustjsonify(
{'error': 'Invalid RPC - must be a string (%s)' % fn_name})
if not fn_name in self.RPC_dict:
return robustjsonify(
{'error': 'Could not find requested RPC "%s"' % fn_name})
found_RPC = self.RPC_dict[fn_name] # Get the RPC we've found.
## Do any validation checks we need to do and return errors if they don't pass.
# If the RPC is disabled, always return a Status 403 (Forbidden)
if found_RPC.validation == 'disabled':
if verbose: print('RPC(): RPC disabled')
abort(403)
# Only do other validation if DataStore and users are included -- NOTE: Any "unknown" validation values are treated like 'none'.
if self.config['USE_DATASTORE'] and self.config['USE_USERS']:
if found_RPC.validation == 'any' and not (
current_user.is_anonymous
or current_user.is_authenticated):
abort(
401
) # If the RPC should be executable by any user, including an anonymous one, but there is no authorization or anonymous login, return a Status 401 (Unauthorized)
elif found_RPC.validation == 'named' and (
current_user.is_anonymous
or not current_user.is_authenticated):
abort(
401
) # Else if the RPC should be executable by any non-anonymous user, but there is no authorization or there is an anonymous login, return a Status 401 (Unauthorized)
elif found_RPC.validation == 'admin': # Else if the RPC should be executable by any admin user, but there is no admin login or it's an anonymous login...
if current_user.is_anonymous or not current_user.is_authenticated:
abort(
401
) # If the user is anonymous or no authenticated user is logged in, return Status 401 (Unauthorized).
elif not current_user.is_admin:
abort(
403
) # Else, if the user is not an admin user, return Status 403 (Forbidden).
# If we are doing an upload...
if found_RPC.call_type == 'upload':
if verbose: print('Starting upload...')
thisfile = request.files[
'uploadfile'] # Grab the formData file that was uploaded.
filename = secure_filename(
thisfile.filename
) # Extract a sanitized filename from the one we start with.
try:
uploaded_fname = os.path.join(
self.datastore.tempfolder,
filename) # Generate a full upload path/file name.
except Exception as E:
errormsg = 'Could not create filename for uploaded file: %s' % str(
E)
raise Exception(errormsg)
try:
thisfile.save(
uploaded_fname) # Save the file to the uploads directory
except Exception as E:
errormsg = 'Could not save uploaded file: %s' % str(E)
raise Exception(errormsg)
args.insert(
0, uploaded_fname) # Prepend the file name to the args list.
# Show the call of the function.
callcolor = ['cyan', 'bgblue']
successcolor = ['green', 'bgblue']
failcolor = ['gray', 'bgred']
timestr = '[%s]' % sc.now(astype='str')
try:
userstr = ' <%s>' % current_user.username
except:
userstr = ' <no user>'
RPCinfo = sc.objdict({
'time': timestr,
'user': userstr,
'module': found_RPC.call_func.__module__,
'name': found_RPC.funcname
})
if self.config['LOGGING_MODE'] == 'FULL':
string = '%s%s RPC called: "%s.%s"' % (
RPCinfo.time, RPCinfo.user, RPCinfo.module, RPCinfo.name)
sc.colorize(callcolor, string, enable=self.colorize)
# Execute the function to get the results, putting it in a try block in case there are errors in what's being called.
try:
if verbose: print('RPC(): Starting RPC...')
T = sc.tic()
result = found_RPC.call_func(*args, **kwargs)
if isinstance(
result, dict
) and 'error' in result: # If the RPC returns an error, return it
return robustjsonify({'error': result['error']})
elapsed = sc.toc(T, output=True)
if self.config['LOGGING_MODE'] == 'FULL':
string = '%s%s RPC finished in %0.2f s: "%s.%s"' % (
RPCinfo.time, RPCinfo.user, elapsed, RPCinfo.module,
RPCinfo.name)
sc.colorize(successcolor, string, enable=self.colorize)
except Exception as E:
if verbose: print('RPC(): Exception encountered...')
shortmsg = str(E)
exception = traceback.format_exc() # Grab the trackback stack
hostname = '|%s| ' % socket.gethostname()
tracemsg = '%s%s%s Exception during RPC "%s.%s" \nRequest: %s \n%.10000s' % (
hostname, RPCinfo.time, RPCinfo.user, RPCinfo.module,
RPCinfo.name, request, exception)
sc.colorize(
failcolor, tracemsg, enable=self.colorize
) # Post an error to the Flask logger limiting the exception information to 10000 characters maximum (to prevent monstrous sqlalchemy outputs)
if self.config['SLACK']:
self.slacknotification(tracemsg)
if isinstance(
E, HTTPException
): # If we have a werkzeug exception, pass it on up to werkzeug to resolve and reply to.
raise E
code = 500 # Send back a response with status 500 that includes the exception traceback.
fullmsg = shortmsg + '\n\nException details:\n' + tracemsg
reply = {
'exception': fullmsg
} # NB, not sure how to actually access 'traceback' on the FE, but keeping it here for future
return make_response(robustjsonify(reply), code)
# If we are doing a download, prepare the response and send it off.
if found_RPC.call_type == 'download':
# To download a file, use `this.$sciris.download` instead of `this.$sciris.rpc`. Decorate the RPC with
# `@RPC(call_type='download')`. Finally, the RPC needs to specify the file and optionally the filename.
# This is done with tuple unpacking. The following outputs are supported from `rpc_function()`
#
# 1 - filename_on_disk
# 2 - BytesIO
# 3 - filename_on_disk, download_filename
# 4- BytesIO, download_filename
#
# Examples return values from the RPC are as follows
#
# 1 - "E:/test.xlsx" (uses "test.xlsx")
# 2 - <BytesIO> (default filename will be generated in this function)
# 3 - ("E:/test.xlsx","foo.xlsx")
# 4 - (<BytesIO>,"foo.xlsx")
#
# On the RPC end, the most common cases would be it might look like
#
# return "E:/test.xlsx"
#
# OR
#
# return Blobject.to_file(), "foo.xlsx"
if verbose: print('RPC(): Starting download...')
if result is None: # If we got None for a result (the full file name), return an error to the client.
return robustjsonify({
'error':
'Could not find resource to download from RPC "%s": result is None'
% fn_name
})
elif sc.isstring(result):
from_file = True
dir_name, file_name = os.path.split(result)
output_name = file_name
elif isinstance(result, io.BytesIO):
from_file = False
bytesio = result
output_name = 'download.obj'
else:
try:
content = result[0]
output_name = result[1]
if sc.isstring(content):
from_file = True
dir_name, file_name = os.path.split(content)
elif isinstance(content, io.BytesIO):
from_file = False
bytesio = content
else:
return robustjsonify(
{'error': 'Unrecognized RPC output'})
except Exception as E:
return robustjsonify(
{'error': 'Error reading RPC result (%s)' % E})
if from_file:
response = send_from_directory(dir_name,
file_name,
as_attachment=True)
response.status_code = 201 # Status 201 = Created
# Unfortunately, we cannot remove the actual file at this point
# because it is in use during the actual download, so we rely on
# later cleanup to remove download files.
else:
response = send_file(bytesio,
as_attachment=True,
attachment_filename=output_name)
response.headers['filename'] = output_name
print(response)
return response # Return the response message.
# Otherwise (normal and upload RPCs),
else:
if found_RPC.call_type == 'upload': # If we are doing an upload....
try:
os.remove(
uploaded_fname
) # Erase the physical uploaded file, since it is no longer needed.
if verbose:
print('RPC(): Removed uploaded file: %s' %
uploaded_fname)
except Exception as E:
if verbose:
print('RPC(): Could not remove uploaded file: %s' %
str(E)) # Probably since moved by the user
if result is None: # If None was returned by the RPC function, return ''.
if verbose: print('RPC(): RPC finished, returning None')
return ''
else: # Otherwise, convert the result (probably a dict) to JSON and return it.
output = robustjsonify(result)
if verbose: print('RPC(): RPC finished, returning result')
return output
def set_metadata(obj):
''' Set standard metadata for an object '''
obj.created = sc.now()
obj.version = cvv.__version__
obj.git_info = cvm.git_info()
return
def run_task(task_id, func_name, args, kwargs):
if kwargs is None: kwargs = {} # So **kwargs works below
if verbose: print('C>> Starting run_task() for %s' % task_id)
# Check if run_task() locked and wait until it isn't, then lock it for
# other run_task() instances in this Celery worker.
# NOTE: We may want to resurrect this, perhaps using the task_id as the lock, if we find out there are
# conflicts with access to the TaskRecords.
# lock_run_task(task_id)
# Find a matching task record (if any) to the task_id.
match_taskrec = datastore.loadtask(task_id)
if match_taskrec is None:
if verbose: print('C>> Failed to find task record for %s' % task_id)
# unlock_run_task(task_id) # uncomment if there are conflicts
return { 'error': 'Could not access Task' }
# Set the TaskRecord to indicate start of the task.
match_taskrec.status = 'started'
match_taskrec.start_time = sc.now()
match_taskrec.pending_time = (match_taskrec.start_time - match_taskrec.queue_time).total_seconds()
# Do the actual update of the TaskRecord.
datastore.savetask(match_taskrec)
if verbose: print('C>> Saved task for %s' % task_id)
# Make the actual function call, inside a try block in case there is
# an exception thrown.
# NOTE: This block is likely to run for several seconds or even
# minutes or hours, depending on the task.
try:
result = task_func_dict[func_name](*args, **kwargs)
match_taskrec.status = 'completed'
if verbose: print('C>> Successfully completed task %s! :)' % task_id)
except Exception as e: # If there's an exception, grab the stack track and set the TaskRecord to have stopped on in error.
error_text = traceback.format_exc()
match_taskrec.status = 'error'
match_taskrec.error_text = error_text
match_taskrec.error_msg = str(e)
result = error_text
if verbose: print('C>> Failed task %s! :(' % task_id)
# Set the TaskRecord to indicate end of the task.
match_taskrec.stop_time = sc.now()
match_taskrec.execution_time = (match_taskrec.stop_time - match_taskrec.start_time).total_seconds()
# Do the actual update of the TaskRecord. Do this in a try / except
# block because this step may fail. For example, if a TaskRecord is
# deleted by the webapp, the update here will crash.
try:
datastore.savetask(match_taskrec)
except Exception as e: # If there's an exception, grab the stack track and set the TaskRecord to have stopped on in error.
error_text = traceback.format_exc()
match_taskrec.status = 'error'
match_taskrec.error_text = error_text
match_taskrec.error_msg = str(e)
result = error_text
if verbose: print('C>> Failed to save task %s! :(' % task_id)
if verbose: print('C>> End of run_task() for %s' % task_id)
# Unlock run-task() for other run_task() instances running on the same
# Celery worker.
# unlock_run_task(task_id) # uncomment if there are conflicts
# Return the result.
return result