def get_context_data(self, **kwargs):
"""Extension of get_context_data
populate the existing metaData values
"""
context = super(RunMetadataDetailView, self).get_context_data(**kwargs)
the_request = self.request
adapter = EMOD_Adapter(the_request.user.username)
my_run = adapter.fetch_runs(run_id=int(kwargs['run_id']))
# if we got here by edit URL, set edit mode.
if 'mode' in kwargs.keys() and kwargs['mode'] == 'edit' and my_run.baseline_key.user.username == the_request.user.username:
context['edit'] = True
try:
context['metaData'] = RunMetaData(my_run)
except RuntimeError:
set_notification('alert-error', '<strong>Error!</strong> Failed to retrieve metadata.', self.request.session)
scenario_id = my_run.baseline_key
if scenario_id:
return redirect("ts_emod_scenario_details", scenario_id=str(scenario_id))
else:
return redirect("ts.index")
return context
def post(self, request, *args, **kwargs):
"""Handle the post of the edit form
"""
my_form = request.POST
adapter = EMOD_Adapter(request.user.username)
my_run = adapter.fetch_runs(run_id=int(kwargs['run_id']))
metaData = RunMetaData(my_run)
changed_flag = 0
for property, value in my_form.iteritems():
if property in vars(metaData):
setattr(metaData, property, value)
changed_flag = 1
# unchecked checkboxes do not register in the form
# so must set to off here if user unchecked is_public
if 'is_public' not in my_form.keys() and metaData.is_public == 'on':
setattr(metaData, 'is_public', 'off')
changed_flag = 1
# is user has made any changes, save it
if changed_flag == 1:
metaData.saveMetaData()
return redirect("ts_emod_run_metadata_details", run_id=int(kwargs['run_id']))
def get_context_data(self, form, **kwargs):
context = super(LaunchTool, self).get_context_data(form, **kwargs)
try:
context['nav_button'] = self.request.session['emod_nav_button']
except KeyError:
pass
# We need either a run id or scenario id (both really)
if 'run_id' in kwargs:
run_id = kwargs['run_id']
if run_id > 0:
self.storage.extra_data['emod_launch_run_id'] = run_id
context['run_named'] = 1
# get the run's name, to prepopulate the name field
adapter = EMOD_Adapter(self.request.user.username)
my_run_id = int(self.storage.extra_data['emod_launch_run_id'])
my_run = adapter.fetch_runs(scenario_id=-1, run_id=int(my_run_id))
context['form'].fields['name'].initial = my_run.name
# save for checking for changes in done method
self.storage.extra_data['old_run_name'] = my_run.name
#else:
# get the specified scenario - error if none specified
try:
if 'scenario_id' in kwargs:
self.storage.extra_data['scenario_id'] = kwargs['scenario_id']
elif 'scenario_id' not in self.storage.extra_data:
self.storage.extra_data['error_invalid_id'] = 1
Exception()
except KeyError:
#If there was no scenario id in the url or storage, this wizard is useless... redirect somewhere else
set_notification('alert-error', 'Error Launching Simulation: Unknown/Invalid run provided. ' +
'Please select a simulation below to launch.', self.request.session)
return context
def saveNote(request, run_id, note_id=None ):
"""Function to save Note DB Objects
"""
if request.method == 'POST':
#note = Note(text=request.POST.get('text'), run_key_id=run_id)
#note.save()
if run_id == None:
run_id = request.POST.get('run_id')
adapter = EMOD_Adapter(request.user.username)
note_id = adapter.save_note(run_id, note=request.POST.get('text'))
if note_id != None:
set_notification('alert-success','<strong>Success!</strong> You have successfully saved the note.', request.session)
else:
set_notification('alert-error','<strong>Error!</strong> There was a problem saving the note.', request.session)
return redirect(request.environ['HTTP_REFERER'])
def run_to_scenario(request, run_id):
""" Function to allow duplication of run DB Objects """
if not request.user.is_authenticated():
set_notification('alert-error', '<strong>Error!</strong> Please log in before duplicating. '
'Run was not duplicated.', request.session)
return redirect("ts_emod_scenario_browse")
else:
# Save a copy of the run to Adapter/DW
try:
adapter = EMOD_Adapter(request.user.username)
old_run = adapter.fetch_runs(run_id=int(run_id), as_object=True)
# create empty scenario
new_scenario = request.session['scenario'] = EMODBaseline(
name=old_run.name + ' copy',
description='Duplicate of ' + old_run.name,
model=DimModel.objects.get(model='EMOD'),
user=DimUser.objects.get_or_create(username=request.user.username)[0]
)
new_scenario.template = DimTemplate.objects.get(id=old_run.template_key_id)
new_scenario.model_version = new_scenario.template.model_version
# get input files for run
file_dict = old_run.get_input_files()
new_scenario.add_file_from_string('campaign', 'campaign.json', file_dict['campaign.json'],
description="Added during duplication from run.")
new_scenario.add_file_from_string('config', 'config.json', file_dict['config.json'],
description="Added during duplication from run.")
# ToDo: get bin input files for run (from run's template)
# - for now, user will have to edit, and location step will provide them
new_scenario.save()
set_notification('alert-success', '<strong>Success!</strong> The run ' + old_run.name
+ ' has been duplicated.', request.session)
except:
print 'Error saving the duplicate run to scenario: %s' % old_run.name
set_notification('alert-error', '<strong>Error!</strong> Error duplicating the run '
+ old_run.name + '.', request.session)
return redirect("ts_emod_scenario_browse")
return redirect("ts_emod_scenario_details", scenario_id=str(new_scenario.id))
def getLocationGraphs(request, location_id=None):
"""
Function to get graph data from DW by url
- Input: location ID
- Output: JSON object of highchart data
- if called without location ID, returns empty dict
"""
if location_id == None:
chart_dict = {}
else:
adapter = EMOD_Adapter()
location_dict = adapter.fetch_locations()
# get HighChart data object
try:
chart_dict = adapter.fetch_weather_chart(location_id, 'chart-div',
start_date=location_dict[int(location_id)]['start_date'],
end_date=location_dict[int(location_id)]['end_date'])
except:
chart_dict = {}
return HttpResponse(json.dumps(chart_dict), mimetype="application/json")
def get_average_daily_value(dim_run,
channel_name,
species_name,
start_year=1,
end_year=None):
"""
:param dim_run:
:type dim_run: DimRun
:param species_name:
:param start_year:
:param end_year:
:return:
"""
adapter = EMOD_Adapter(dim_run.baseline_key.user.username)
data = adapter.fetch_data(dim_run.dimexecution_set.all()[0],
channel_name=channel_name,
channel_type=species_name)
data = data.values()[0]
# Start and End years start from 1, not from 0
start_year -= 1
if start_year < 0:
start_year = 0
end_year -= 1
if end_year < 0:
return None
if end_year is None:
data = data[int(start_year*365):]
else:
if len(data) < int(end_year*365) + 365:
return None
data = data[int(start_year*365):int(end_year*365) + 365]
if len(data) == 0:
return None
return sum(data) / len(data)
def get_context_data(self, **kwargs):
"""Extension of get_context_data
Add context data to drive detail view.
"""
context = super(TemplateDetailView, self).get_context_data(**kwargs)
context['selected_scenario'] = self.request.session['selected_scenario']
adapter = EMOD_Adapter()
my_template_id = kwargs['template_id']
my_temp_list = adapter.fetch_template_list()
for id in my_temp_list:
if id == int(my_template_id):
context['template_name'] = my_temp_list[id]['name']
context['template_description'] = my_temp_list[id]['description']
context['template_campaign_description'] = my_temp_list[id]['files']['campaign.json']['description']
context['template_config_description'] = my_temp_list[id]['files']['config.json']['description']
my_loc_list = adapter.fetch_locations()
for loc_id in my_loc_list:
if loc_id == my_temp_list[id]['location_ndx']:
context['template_location_name'] = my_loc_list[loc_id]['place'] + ', ' + my_loc_list[loc_id]['country']
context['template_location_start_date'] = my_loc_list[loc_id]['start_date']
context['template_location_end_date'] = my_loc_list[loc_id]['end_date']
context['template_location_resolution'] = my_loc_list[loc_id]['resolution']
context['template_location_link'] = my_loc_list[loc_id]['link']
my_temp = adapter.fetch_template(int(kwargs['template_id']))
my_config = ast.literal_eval(my_temp['config.json'])
context['template_campaign_warning'] = my_config['parameters']['Enable_Interventions']
context['template_config'] = re.sub("\r{2,}", '\r', my_temp['config.json'])
context['template_campaign'] = re.sub("\r{2,}", '\r', my_temp['campaign.json'])
return context
def done(self, form_list, **kwargs):
if 'error_invalid_id' in self.storage.extra_data:
self.storage.reset()
set_notification('alert-error', 'Error Launching Simulation: Unknown/Invalid run provided. ' +
'Please select a simulation below to launch.', self.request.session)
return redirect("ts_emod_scenario_browse")
if 'scenario_id' in self.storage.extra_data:
scenario_id = int(self.storage.extra_data['scenario_id'])
else:
Exception()
adapter = EMOD_Adapter(self.request.user.username)
if 'emod_launch_run_id' in self.storage.extra_data:
my_run_id = int(self.storage.extra_data['emod_launch_run_id'])
my_run = adapter.fetch_runs(scenario_id=-1, run_id=int(my_run_id))
# check for name changes from user
start_data = self.get_cleaned_data_for_step('start')
if self.storage.extra_data['old_run_name'] != start_data['name']:
my_run.name = start_data['name']
my_run.save()
else:
# get the scenario
self.storage.extra_data['scenario'] = EMODBaseline.from_dw(pk=scenario_id)
my_config = ast.literal_eval(self.storage.extra_data['scenario'].get_file_by_type('config').content)
try:
my_campaign = ast.literal_eval(self.storage.extra_data['scenario'].get_file_by_type('campaign').content)
except AttributeError:
# if file list was returned, use last file
file_list = self.request.session['scenario'].get_file_by_type('campaign')
my_campaign = ast.literal_eval(file_list[0].content)
my_campaign_length = len(my_campaign['Events'])
###
# create a new run instance
if my_campaign_length > 0:
with_interventions = "with interventions "
else:
with_interventions = ""
my_simulation_duration = my_config['parameters']['Simulation_Duration']
## Set the run start_date based on location and config's start_time
my_start_date = \
datetime.datetime.strptime(
self.storage.extra_data['scenario'].template.climate_start_date,
'%Y-%m-%d').date() \
+ datetime.timedelta(days=my_config['parameters']['Start_Time'])
# Initialize the run
my_run = adapter.save_run(scenario_id=scenario_id,
template_id=int(self.storage.extra_data['scenario'].template.id),
start_date=my_start_date,
duration=my_simulation_duration,
name=self.get_cleaned_data_for_step('start')['name'],
description='Launch Tool: ' + self.storage.extra_data['scenario'].name
+ ': Run ' + with_interventions + str(datetime.datetime.now()),
location_ndx=self.storage.extra_data['scenario'].template.location_key.id,
timestep_interval=1,
run_id=-1,
as_object=True)
my_run.baseline_key_id = scenario_id
my_run.save()
if settings.DEBUG:
print "DEBUG: LaunchTool: run id: ", my_run.id
# add in JCD for config file
changes = []
newdict = copy.deepcopy(my_config)
newdict['config.json/parameters'] = newdict.pop('parameters')
changes.append(Change.node(name='config.json', node=[newdict], mode='-'))
# add in JCD for campaign file
if my_campaign_length > 0:
newdict = copy.deepcopy(my_campaign)
newdict['campaign.json/Use_Defaults'] = newdict.pop('Use_Defaults')
newdict['campaign.json/Events'] = newdict.pop('Events')
changes.append(Change.node(name='campaign.json', node=[newdict], mode='-'))
my_run.jcd = JCD.from_changes(changes)
my_run.save()
### Launch the run
# 5853 - hard-code to 1 for now
#reps_per_exec = int(self.get_cleaned_data_for_step('start')['reps_per_exec'])
reps_per_exec = 1
# If this is a representative based scenario, then set it to non-editable
representative_scenario = RepresentativeScenario.objects.filter(emod_scenario_id=scenario_id)
if representative_scenario:
representative_scenario[0].is_editable = False
representative_scenario[0].save()
# submit returns tuple (success, message)
try:
status = submit(my_run, user=self.request.user, manifest=True, reps_per_exec=reps_per_exec)
set_notification('alert-success', '<strong>Success!</strong> Run launched.',
self.request.session)
except (RuntimeError, TypeError, AssertionError), e:
set_notification('alert-error', '<strong>Error!</strong> ' + str(e.message), self.request.session)
def process_step(self, form):
""" Method to handle "after Next-click" processing of steps """
# set the flag that determines when to save the config to the scenario
change_config = 0
# set the flag that determines when to save the scenario
change_scenario = 0
adapter = EMOD_Adapter(self.request.user.username)
if self.steps.current == 'config':
if self.request.session['scenario_config']['parameters']['Simulation_Duration'] != \
form.cleaned_data['Simulation_Duration']:
self.request.session['scenario_config']['parameters']['Simulation_Duration'] = \
form.cleaned_data['Simulation_Duration']
change_config = 1
if self.request.session['scenario_config']['parameters']['Simulation_Type'] != \
form.cleaned_data['Simulation_Type']:
self.request.session['scenario_config']['parameters']['Simulation_Type'] = \
form.cleaned_data['Simulation_Type']
change_config = 1
if self.request.session['scenario_config']['parameters']['Start_Time'] != form.cleaned_data['Start_Time']:
self.request.session['scenario_config']['parameters']['Start_Time'] = form.cleaned_data['Start_Time']
change_config = 1
if self.request.session['scenario'].name != form.cleaned_data['name']:
self.request.session['scenario'].name = form.cleaned_data['name']
change_scenario = 1
if self.request.session['scenario'].description != form.cleaned_data['description']:
self.request.session['scenario'].description = form.cleaned_data['description']
change_scenario = 1
# Workaround for bug #5626 config file is not saved if user doesn't change Simulation Duration on
# Step 2 of 9: Configure Simulation
change_config = 1
# 6230: redirect to Intervention Tool (if user clicked "Skip to Intervention Tool Button")
# Set session variable here, so dispatch at beginning of next step knows to redirect (wizard won't allow
# redirect here to work.
if 'jump_to_intervention_tool' in self.request.POST.keys():
self.request.session['jump_to_intervention_tool'] = 1
if self.steps.current == 'species':
species_list = form.cleaned_data['species']
# if the list NOT matches the old list, update it
if species_list != self.request.session['scenario_config']['parameters']['Vector_Species_Names']:
self.request.session['scenario_config']['parameters']['Vector_Species_Names'] = species_list
change_config == 1
# check also for changes in the Vector Parameters (vector list may be the same)
my_json = dict(form.data)
# Gather parameter sets for all species in names list.
parameter_dict = {}
for species in species_list:
# add each Vector to Params list
my_dict = {}
for key in sorted(my_json.keys()): # sorted so Habitat_Type/Required_Habitat_Factor order preserved
if str(species) + '__json_' in key:
if type(my_json[key]) == list:
my_value = my_json[key][0]
else:
my_value = my_json[key]
if type(my_value) not in (float, int):
try:
my_value = int(str(my_value))
except (ValueError, TypeError):
try:
my_value = float(str(my_value))
except (ValueError, TypeError):
pass
if 'Required_Habitat_Factor' in key.split('__json_')[1]:
if my_value == '':
continue
if 'Required_Habitat_Factor' in my_dict.keys():
my_dict['Required_Habitat_Factor'].append(my_value)
else:
my_dict.update({'Required_Habitat_Factor': [my_value]})
elif 'Habitat_Type' in key.split('__json_')[1]:
if 'Habitat_Type' in my_dict.keys():
my_dict['Habitat_Type'].append(my_value)
else:
my_dict.update({'Habitat_Type': [my_value]})
elif key.split('__json_')[1] != 'obj':
my_dict.update({key.split('__json_')[1]: my_value})
parameter_dict.update({species: my_dict})
if self.request.session['scenario_config']['parameters']['Vector_Species_Params'] != parameter_dict:
self.request.session['scenario_config']['parameters']['Vector_Species_Params'] = parameter_dict
change_config = 1
if self.steps.current == 'parasite':
my_fields = json.loads(form.cleaned_data['json'])
for key in my_fields:
my_value = my_fields[key]['value']
if type(my_value) in (str, unicode):
try:
my_value = int(my_value)
except ValueError:
try:
my_value = float(my_value)
except ValueError:
pass
if my_value != self.request.session['scenario_config']['parameters'][key]:
self.request.session['scenario_config']['parameters'][key] = my_value
change_config = 1
if self.steps.current == 'scaling_factors':
my_value = form.cleaned_data['x_Temporary_Larval_Habitat']
if type(my_value) in (str, unicode):
try:
my_value = int(my_value)
except ValueError:
try:
my_value = float(my_value)
except ValueError:
pass
if my_value != self.request.session['scenario_config']['parameters']['x_Temporary_Larval_Habitat']:
self.request.session['scenario_config']['parameters']['x_Temporary_Larval_Habitat'] = my_value
change_config = 1
# populate new scenario with template data
# or with existing scenario data if this call is for Editing a scenario
if (self.steps.current == 'location' and form.cleaned_data['template_id'])\
and ('template_id' not in self.storage.extra_data.keys()
or self.storage.extra_data['template_id'] != form.cleaned_data['template_id']):
# todo: some of this is either edit-mode or new-mode: sort out later (depending on availability of data)
template_id = int(form.cleaned_data['template_id'])
if 'template_id' in self.storage.extra_data \
and template_id != self.storage.extra_data['template_id']:
pass # location_change = 1
else:
# first time through wizard, not a location change
# location_change = 0
# save schema
self.request.session['schema.json'] = ConfigData.objects.filter(type='schema',
name='emod-v1.5-schema.txt')[0].json
# Set name here with dummy name as adding a file will attempt to save the scenario,
# which fails if name is null
if self.request.session['scenario'].name is None:
self.request.session['scenario'].name = ''
self.request.session['scenario'].description = ''
# check for campaign file...
try:
# if it exists, do nothing
self.request.session['scenario'].get_file_by_type('campaign')
except ObjectDoesNotExist:
# else: add in empty campaign file
self.request.session['scenario'].add_file_from_string('campaign',
'campaign.json',
str({"Events": []}),
description=self.steps.current)
my_template_obj = DimTemplate.objects.get(id=template_id)
self.request.session['scenario'].model_version = my_template_obj.model_version
self.request.session['scenario'].dimbaseline.model_version = my_template_obj.model_version
self.request.session['scenario'].template_id = template_id
self.request.session['scenario'].template = my_template_obj
self.request.session['scenario'].save()
location_id = my_template_obj.location_key_id
self.request.session['scenario'].template_id = template_id
self.request.session['scenario'].template = my_template_obj
# needed for editing
if self.request.session['scenario'].dimbaseline is not None:
self.request.session['scenario'].dimbaseline.template = my_template_obj
self.request.session['scenario'].dimbaseline.template_id = template_id
change_scenario = 1
# Populate the step data with the chosen location's data
self.storage.extra_data.update({'template_id': template_id})
# populate config to the session for multiple uses later
template_config = ast.literal_eval(my_template_obj.get_file_content('config.json'))
if 'edit_scenario' in self.storage.extra_data.keys() \
and 'config' not in self.request.session['scenario'].get_missing_files():
# use scenario's config file
try:
self.request.session['scenario_config'] = \
ast.literal_eval(self.request.session['scenario'].get_file_by_type('config').content)
except AttributeError:
# if query set returned, use first file in "list"
file_list = self.request.session['scenario'].get_file_by_type('config')
self.request.session['scenario_config'] = \
ast.literal_eval(file_list[0].content)
else:
# use template's (or parent scenario's) config file
self.request.session['scenario_config'] = copy.deepcopy(template_config)
self.storage.extra_data.update({'scenario_template_config': template_config})
change_config = 1
#########################
### Add default files to scenario
# todo: stop using template zips, when climate files are available elsewhere
print my_template_obj.climate_url
self.storage.extra_data.update({'location_zip_link': my_template_obj.climate_url})
# Do we cache zip to temp dir first time, and always access them from there (if they exist)
# FILE_UPLOAD_TEMP_DIR
# setup work directory
#my_directory = os.path.join(settings.MEDIA_ROOT, 'uploads/expert_emod/')
#my_directory = os.path.join(FILE_UPLOAD_TEMP_DIR, 'ts_emod/')
#if not os.path.exists(my_directory):
# os.makedirs(my_directory)
#inStream = urllib2.urlopen('http://dl-vecnet.crc.nd.edu/downloads/wh246s153')
#inStream = urllib2.urlopen('https://dl.vecnet.org/downloads/wh246s153')
if 'location_zip_link' in self.storage.extra_data:
if settings.DEBUG is True:
now = datetime.datetime.now()
print now, " DEBUG: getting zip file: ", self.storage.extra_data['location_zip_link']
url = urlopen(self.storage.extra_data['location_zip_link'])
zipfile = ZipFile(StringIO(url.read()))
for zip_file_name in zipfile.namelist():
if settings.DEBUG is True:
now = datetime.datetime.now()
print now, " DEBUG: handling file: ", zip_file_name
my_file = zipfile.open(zip_file_name)
my_name = ntpath.basename(zip_file_name)
# determine which file type this is
# my_name contains 'demographics' ? (use compiled, store both?) Honiara_demographics.static.compiled.json Honiara_demographics.json
"""
'air binary',
'air json',
'humidity binary',
'humidity json',
'land_temp binary',
'land_temp json',
'rainfall binary',
'rainfall json',
Honiara_demographics.compiled.json
Honiara_demographics.json
Honiara_demographics.static.compiled.json
Honiara_demographics.static.json
Honiara_humidity_daily10y.bin
Honiara_humidity_daily10y.bin.json
Kenya_Nyanza_2.5arcminhumid_1365118879_climateheader.json
Honiara_rainfall_daily10y.bin
Honiara_rainfall_daily10y.bin.json
Honiara_temperature_daily10y.bin
Honiara_temperature_daily10y.bin.json
"""
my_type = None
if '.md5' in my_name:
continue
elif 'demographics' in my_name or 'Demographics' in my_name:
if 'compiled' in my_name:
# use in scenario
my_type = 'demographics'
else:
# save to storage (to allow user to see contents)
self.storage.extra_data['demographics'] = my_file
elif '.json' in my_name and '.json.bin' not in my_name:
# 'json' files
if 'humid' in my_name:
my_type = 'humidity json'
elif 'rain' in my_name:
my_type = 'rainfall json'
elif 'temp' in my_name or 'tmean' in my_name:
my_type = 'air json'
else:
# must be a binary file
if 'humid' in my_name:
my_type = 'humidity binary'
elif 'rain' in my_name:
my_type = 'rainfall binary'
elif 'temp' in my_name or 'tmean' in my_name:
my_type = 'air binary'
if my_type is not None:
if 'binary' in my_type:
self.request.session['scenario'].add_file_from_string(my_type, my_name,
my_file.read(),
description=self.steps.current)
else:
self.request.session['scenario'].add_file_from_string(my_type, my_name,
my_file.read(),
description=self.steps.current)
change_scenario = 1
# todo: fix to allow separate air and land temp files
# for now: use same files for air temp and land temp
if my_type in ('air binary', 'air json'):
my_type = my_type.replace('air', 'land_temp')
self.request.session['scenario'].add_file_from_string(my_type, my_name,
"no land temp file",
description=self.steps.current)
### END if zip file is none
# could save here to free up memory from the object file storage
# but it fails without a name
#if change_scenario == 1:
# self.request.session['scenario'].save()
### END Zip/Input File handling
######################
# config step data:
self.storage.set_step_data('config', {u'config-name': [self.request.session['scenario']._name],
u'config-description': [self.request.session['scenario'].description],
u'config-Start_Time': [self.request.session['scenario_config']['parameters']['Start_Time']],
u'config-Simulation_Duration':
[self.request.session['scenario_config']['parameters']['Simulation_Duration']],
u'config-Simulation_Type':
[self.request.session['scenario_config']['parameters']['Simulation_Type']],
})
# climate step data:
self.storage.set_step_data('climate', {u'climate-location': [location_id]})
# demographic step data:
self.storage.set_step_data('demographic', {u'demographic-location': [location_id]})
# parasite
for step_name in ["vector", "parasite"]:
# get db config for the step
my_json = ConfigData.objects.filter(type='JSONConfig', name=step_name)[0].json
# wizard values based on config + template values
my_wiz = {u'orig_json_obj': [my_json]}
my_json = json.loads(my_json)
for key in my_json.keys():
try:
# = scenario value OR template value
# change into wizard format step name + -json_ + key name
my_wiz.update({u'' + step_name + '-json_'
+ key: [u'' + str(self.request.session['scenario_config']['parameters'][key])]})
except KeyError:
pass
# insert into wizard storage
self.storage.set_step_data(step_name, my_wiz)
# Scaling step data:
self.storage.set_step_data('scaling_factors',
{u'scaling_factors-x_Temporary_Larval_Habitat':
[self.request.session['scenario_config']['parameters']['x_Temporary_Larval_Habitat']]})
# save any changes made to the scenario config file
if change_config == 1 and self.steps.current != 'location':
self.request.session['scenario'].add_file_from_string('config', 'config.json',
str(self.request.session['scenario_config']),
description=self.steps.current)
change_scenario = 1
if change_scenario == 1 and self.steps.current != 'location':
# don't save until config step (name and description will be populated there.
try:
my_id, completed = self.request.session['scenario'].save()
set_notification('alert-success', 'The simulation was saved. ', self.request.session)
except KeyError:
set_notification('alert-error', 'Error: The simulation was not saved. ', self.request.session)
###########################
### Create a run with scenario settings
# - launch it
# - display status
# ??? Do we want to force/allow user to add name/description to these runs?
# ??? Cap duration for initial run? 5 years?
if self.steps.current == 'run':
# create a new run instance
adapter = EMOD_Adapter(self.request.user.username)
my_template = DimTemplate.objects.get(id=self.request.session['scenario'].template.id)
my_start_date = \
datetime.datetime.strptime(
my_template.climate_start_date,
'%Y-%m-%d').date() \
+ datetime.timedelta(days=self.request.session['scenario_config']['parameters']['Start_Time'])
my_run = adapter.save_run(
template_id=int(self.request.session['scenario'].template.id),
start_date=my_start_date,
duration=100, # 1825, 5 years
#=self.request.session['scenario_config']['parameters']['Simulation_Duration'],
name=form.cleaned_data['name'], # self.request.session['scenario'].name + ': Test Run '
description='Run by New Simulation Wizard',
location_ndx=my_template.location_key.id,
timestep_interval=1,
run_id=-1, # run_id,
as_object=True)
my_run.scenario_key_id = self.request.session['scenario'].id
my_run.save()
if settings.DEBUG:
print "DEBUG: line 890 BaselineWiz: run id: ", my_run.id
# add in JCD for it for config file
changes = []
newdict = copy.deepcopy(self.request.session['scenario_config'])
newdict['config.json/parameters'] = newdict.pop('parameters')
changes.append(Change.node(name='config.json', node=[newdict], mode='-'))
my_run.jcd = JCD.from_changes(changes)
my_run.save()
### Launch the run
# save launch info to extra data todo: this should eventually go into success block below
self.storage.extra_data['last_launched_run'] = my_run.id
# submit returns tuple (success, message)
status = submit(my_run, user=self.request.user, manifest=True, reps_per_exec=1)
try:
if status[0] is True:
set_notification('alert-success', '<strong>Success!</strong> Test Run launched.',
self.request.session)
else:
set_notification('alert-error', '<strong>Error!</strong> ' + status[1], self.request.session)
except TypeError:
pass
return self.get_form_step_data(form)
def get_context_data(self, form, **kwargs):
"""Extension of the get_context_data method of the NamedUrlSessionWizardView.
Select/process data based on which step of the Form Wizard it's called for.
- Date: passes existing start_date, end_date values or nothing then template will use min and max.
- Preview gets all wizard step data gathered so far.
"""
context = super(BaselineWizardView, self).get_context_data(form=form, **kwargs)
# All steps:
if 'edit_scenario' in self.storage.extra_data:
# if we're in edit mode, let templates know ("Start Over" vs "Cancel Edit" button)
context['edit_scenario'] = self.storage.extra_data['edit_scenario']
######### Start code for specific steps #########
if self.steps.current == 'location':
the_request = self.request
adapter = EMOD_Adapter(self.request.user.username)
templates = adapter.fetch_template_list() # get for description
for key in templates.keys():
if 'edit_scenario' in self.storage.extra_data \
and 'scenario' in self.request.session.keys() \
and self.request.session['scenario'].template is not None \
and self.request.session['scenario'].template.id is not None \
and self.request.session['scenario'].template.id == key:
# set the checked option based on the scenario being edited
templates[key]['checked'] = 1
elif 'location' in self.storage.data['step_data'].keys()\
and 'location-template_id' in self.storage.data['step_data'][u'location'].keys()\
and unicode(key) == \
self.storage.data['step_data'][u'location'][u'location-template_id'][0]:
# set checked option based on wizard value already saved
templates[key]['checked'] = 1
# For now: limit list to Solomon and Kenya templates
templates_a = {}
templates_b = {}
templates_c = {}
templates_d = {}
templates_e = {}
# reorder the templates so Vietnam 1st, Kenya 2nd, Solomon 3rd
for key in templates.keys():
if 'Vietnam' in templates[key]['name']:
templates_a.update({key: templates[key]})
for key in templates.keys():
if 'Kenya' in templates[key]['name']:
templates_b.update({key: templates[key]})
for key in templates.keys():
if 'Solomon' in templates[key]['name']:
templates_c.update({key: templates[key]})
for key in templates.keys():
if 'Uganda' in templates[key]['name']:
templates_d.update({key: templates[key]})
for key in templates.keys():
if 'Bougainville' in templates[key]['name']:
templates_e.update({key: templates[key]})
pager_size = the_request.POST.get('pager_size')
if pager_size is None:
pager_size = 10
else:
pager_size = int(pager_size)
pager_offset = the_request.POST.get('pager_offset')
if pager_offset is None:
pager_offset = 0
else:
pager_offset = int(pager_offset)
pager_group = the_request.POST.get('pager_group')
if pager_group is None:
pager_group = 0
else:
try:
pager_group = int(pager_group)
except TypeError:
pager_group = 0
template_count = len(templates)
pager_count = template_count / pager_size
if template_count % pager_size != 0:
pager_count += 1
context['pager_offset'] = pager_offset
context['pager_size'] = pager_size
context['pager_group'] = pager_group
context['pager_count'] = range(1, pager_count + 1)
context['pager_max'] = pager_count
context['templates_a'] = templates_a
context['templates_b'] = templates_b
context['templates_c'] = templates_c
context['templates_d'] = templates_d
context['templates_e'] = templates_e
context['template_count'] = template_count
context['current_start'] = pager_offset * pager_size + 1
context['current_stop'] = min(template_count, pager_offset * pager_size + pager_size)
return context
if self.steps.current == 'climate':
my_template = DimTemplate.objects.get(id=self.storage.extra_data['template_id'])
context['template'] = my_template
# set up the context to include the files (if any) attached to the scenario
my_types = [
'air binary',
#'air json',
'humidity binary',
#'humidity json',
#'land_temp binary',
#'land_temp json',
'rainfall binary']
#'rainfall json']
# get scenario files: types/names
context['climate_files'] = {}
for my_file in self.request.session['scenario'].get_files():
# my_file[0] id
# my_file[1] name
# my_file[2] type
if my_file[2] in my_types:
context['climate_files'].update({my_file[2].split(' ')[0]: my_file[1]})
context['climate_files'] = sorted(context['climate_files'].iteritems())
context['scenario_id'] = self.request.session['scenario'].id
my_template = DimTemplate.objects.get(id=self.storage.extra_data['template_id'])
context['template'] = my_template
if self.steps.current == 'demographic':
my_template = DimTemplate.objects.get(id=self.storage.extra_data['template_id'])
context['template'] = my_template
if self.steps.current == 'species':
###
# Get list of species user can base NEW species creation on (drop-down menu)
# and to use for adding to a simulation
# get from template
try:
context['species_templates'] = \
self.storage.extra_data['scenario_template_config']['parameters']['Vector_Species_Params']
except KeyError:
pass
###
# Modify the above list to make the "select from" sources
species_list = []
try:
# turn into objects
for key, value in context['species_templates'].items():
json_string = '{"' + key + '":' + json.dumps(value) + "}"
species_list.append(Species(name=key, is_template=1, is_public=0, json=json_string,
created_by=self.request.user))
except KeyError:
pass
# Add in public and user's own custom species objects from DB
for species in Species.objects.filter(Q(is_public=1) | Q(created_by=self.request.user)):
species_list.append(species)
# This serves as the "from template", "user's custom" and "public" species available
context['species_list'] = species_list
###
# Populate the already chosen list
# # Get Baseline or Template ID for passing to SpeciesCreate View
# # because wizard storage won't be available in SpeciesCreate View
my_scenario_id = self.storage.extra_data.get('scenario_id')
my_species = []
try:
my_species.extend(self.request.session['scenario_config']['parameters']['Vector_Species_Names'])
except (KeyError, TypeError):
pass
my_species = sorted(set(my_species))
context['species_chosen'] = {u'species-species': json.dumps(my_species),
'scenario_id': my_scenario_id,
u'orig_json_obj': ConfigData.objects.filter(
type='JSONConfig', name='default_emod_vector')[0].json}
context['species_chosen_values'] = \
json.dumps(self.request.session['scenario_config']['parameters']['Vector_Species_Params'])
if self.steps.current == 'parasite' or self.steps.current == "vector":
step_name = self.steps.current
# build titles for template from name, misc
my_object = ConfigData.objects.filter(type='JSONConfig', name=step_name)[0]
context['step_title'] = step_name.title() + " " + my_object.misc.split(":")[1].title()
context['description'] = my_object.description
# if the user has not already been through this step
# populate the form with the template values.
if not self.storage.get_step_data(step_name):
try:
context['template_values'] = self.request.session['scenario_config']['parameters']
except KeyError:
pass
if self.steps.current == 'run':
form.fields['name'].initial = 'Test Run ' + str(datetime.datetime.now())
if self.steps.current == 'review':
# get list of runs for this scenario
adapter = EMOD_Adapter(self.request.user.username)
run_list = DimRun.objects.filter(baseline_key=self.request.session['scenario'].id)
if len(run_list) > 0:
# sort descending by id (for those old runs that all have the same old time_created
run_list = sorted(run_list, key=lambda x: x.id, reverse=True)
# sort descending by time_saved
run_list = sorted(run_list, key=lambda x: x.time_created, reverse=True)
# get most recent run, is it still running?
my_run = run_list[0]
# check to see if a run is currently running
status = adapter.run_status(my_run.id)
if status is None:
my_run.my_completed = None
else:
my_run.my_completed = status[0]
my_run.my_failed = status[2]
if status[0] > 0:
context['scenario_has_results'] = 1 # this sets if any of the runs here has results
my_run.my_total = status[1]
my_run.my_percent_complete = float(status[0]) / float(status[1]) * 100
my_run.my_percent_failed = float(status[2]) / float(status[1]) * 100
my_run.errors = adapter.fetch_errors(my_run.id)
# get the results for the last run(s) if it's finished
context['my_run'] = my_run
# #6329 - pass in scenario for display of info
context['scenario'] = self.request.session['scenario']
my_config = self.request.session['scenario'].get_file_by_type('config').content
context['Simulation_Duration'] = ast.literal_eval(my_config)['parameters']['Simulation_Duration']
if self.steps.current == 'run':
# check for existing runs in this scenario
if 'scenario' in self.request.session.keys():
my_runs = DimRun.objects.filter(baseline_key=self.request.session['scenario'].id)
if len(my_runs) > 0:
context['has_runs'] = len(my_runs)
# populate the step data so if the skip button is used,
# the wizard doesn't skip back to here upon wizard submission (skip isn't a submit, just goto_step)
self.storage.set_step_data('run', {u'baseline_wizard_view-current_step': [u'run']})
return context
def get_context_data(self, **kwargs):
"""Extension of get_context_data
Add context data to drive menu nav highlights, breadcrumbs and pagers.
"""
context = super(ScenarioBrowseView, self).get_context_data(**kwargs)
the_request = self.request
context['nav_button'] = 'scenario_browse'
pager_size = the_request.POST.get('pager_size') or the_request.GET.get('pager_size')
if pager_size is None:
pager_size = 10
else:
pager_size = int(pager_size)
# Get list of folders in this folder (if no current folder, include folders with no parent)
if 'folder_id' in kwargs.keys():
current_folder = kwargs['folder_id'] or the_request.POST.get('folder_id') or the_request.GET.get('folder_id') or None
context['current_folder'] = Folder.objects.get(pk=current_folder)
else:
current_folder = None
# get a list of all scenarios in order to get count of sims in each folder
scenario_list_all = list(DimBaseline.objects.filter(user=DimUser.objects.get(username=self.request.user.username),
is_deleted=False))
my_count = {}
for scen in scenario_list_all:
if scen.folder_id in my_count.keys():
my_count[scen.folder_id] += 1
else:
my_count[scen.folder_id] = 1
# create a dictionary of children (keys are parents, value is list of children)
folder_list_all = list(Folder.objects.filter(user=DimUser.objects.get(username=self.request.user.username),
is_deleted=False))
my_dict = defaultdict(list)
for folder in folder_list_all:
if folder.id in my_count.keys():
counter = ' (' + str(my_count[folder.id]) + ')'
else:
counter = ''
if folder.parent is None:
my_dict[0].append({'id': folder.id, 'name': folder.name, 'child_count': counter})
else:
my_dict[folder.parent.id].append({'id': folder.id, 'name': folder.name, 'child_count': counter})
current_found = 0 # Set flag that deterimines if the current folder has been visited in the tree
if None in my_count.keys():
counter_root = ' (' + str(my_count[None]) + ')'
else:
counter_root = ''
folder_tree = '{title: "My Simulations' + counter_root + '", folder: true, expanded: true'
if current_folder is None:
folder_tree += ', active: true'
current_found = 1
# context['folder_tree'] = '{title: "My Tororo Folder full of Simulations (and folders) in home folder ", folder: true }, ' \
# '{title: "Folder 2", folder: true, ' \
# 'children: [ ' \
# '{ title: "Sub-item 2.1", folder: true }, ' \
# '{ title: "Sub-item 2.2" }] }, ' \
# '{ title: "Item 3" }'
# without root:
# context['folder_tree'] = '{title: "Solomon Islands", folder: true}, {title: "Second folder", folder: true, children: [ {title: "subfolder", folder: true}] }'
#folder_tree = add_children(0, my_dict)
# with root:
# context['folder_tree'] = '{title: "My Simulations", folder: true, children: [ {title: "Solomon Islands", folder: true}, {title: "Second folder", folder: true, children: [ {title: "subfolder", folder: true}] }] }'
folder_tree += add_children(0, my_dict, current_folder, current_found) + '}'
context['folder_tree'] = str(folder_tree)
# Get list of scenarios
scenario_list = list(DimBaseline.objects.filter(user=DimUser.objects.get(username=self.request.user.username),
folder=current_folder,
is_deleted=False))
if scenario_list is None:
return context
# sort descending by id (for those old scenarios that all have the same old time_created
scenario_list = sorted(scenario_list, key=lambda x: x.id, reverse=True)
# sort descending by time_saved (version)
scenario_list = sorted(scenario_list, key=lambda x: x.last_modified, reverse=True)
# merge folders into scenario list
# - show folders in file list
#scenario_list = folder_list + scenario_list
# Flag scenarios that are representative
for scenario in scenario_list:
# Hack for now. I don't remember if it is still needed, but I will fix it later. Not currently important.
if scenario.description == "Made with representative workflow" and not scenario.metadata:
scenario.metadata = json.dumps({'representative': ''})
scenario.save()
if scenario.metadata:
metadata = json.loads(scenario.metadata)
if 'representative' in metadata:
scenario.is_representative = True
if 'is_complete' in metadata['representative']:
scenario.representative_is_complete = metadata['representative']['is_complete']
else:
scenario.representative_is_complete = False
scenario.name = derive_autoname(scenario)
else:
scenario.is_representative = False
paginator = Paginator(scenario_list, pager_size)
page = int(the_request.GET.get('page') or 1)
try:
scenarios = paginator.page(page)
except PageNotAnInteger:
# If page is not an integer, deliver first page.
scenarios = paginator.page(1)
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
scenarios = paginator.page(paginator.num_pages)
scenario_count = len(scenario_list)
context['pager_size'] = pager_size
context['scenarios'] = scenarios
context['scenario_range'] = range(paginator.num_pages)
context['scenario_count'] = scenario_count
context['current_start'] = (page-1)*pager_size + 1
context['current_stop'] = min(scenario_count, (page-1)*pager_size + pager_size)
context['my_username'] = self.request.user.username
# get locations (need name from dict by id)
adapter = EMOD_Adapter(self.request.user.username)
template_list = adapter.fetch_template_list()
location_dict = adapter.fetch_locations() # gets list based on EMOD_buffer list in model_adapter.py
# determine which step edit buttons link to
step_list = [i[0] for i in named_baseline_forms]
for scenario in scenario_list:
if scenario._meta.object_name != 'Folder':
try:
# check to see if it has a campaign file (besides the empty default)
if scenario.is_approved:
my_scenario = EMODBaseline.from_dw(pk=scenario['id'])
try:
scenario_campaign = json.dumps(ast.literal_eval(my_scenario.get_file_by_type('campaign').content),
sort_keys=True, indent=4, separators=(',', ': '))
except (AttributeError, ObjectDoesNotExist):
try:
# if file list was returned, use last file
scenario_campaign = json.dumps(ast.literal_eval(
my_scenario.get_file_by_type('campaign')[my_scenario.get_file_by_type('campaign').count()
- 1].content), sort_keys=True, indent=4,
separators=(',', ': '))
except ObjectDoesNotExist:
pass
if len(json.loads(scenario_campaign)['Events']) > 0:
scenario['has_interventions'] = 1
if scenario.template:
scenario.location_name = str(DimTemplate.objects.get(id=scenario.template.id).location_key)
# add model version to scenario
scenario.model_version = DimTemplate.objects.get(id=scenario.template.id)\
.model_version.replace('emod ', '')
except:
pass
return context
def get_context_data(self, form, **kwargs):
"""Extension of the get_context_data method of the NamedUrlSessionWizardView.
Select/process data based on which step of the Form Wizard it's called for.
- Date: passes existing start_date, end_date values or nothing then template will use min and max.
- Preview gets all wizard step data gathered so far.
"""
context = super(ScenarioCreateByTemplate, self).get_context_data(form=form, **kwargs)
context["nav_button"] = "ts_ScenarioCreateByTemplate_step" # set flag to activate nav menu highlighting
######### Start code for specific steps #########
if self.steps.current == "location":
the_request = self.request
adapter = EMOD_Adapter(self.request.user.username)
templates = adapter.fetch_template_list() # get for description
if "folder_id" in kwargs.keys():
context["current_folder"] = kwargs["folder_id"]
# For now: limit list to Solomon and Kenya templates
templates_a = {}
templates_b = {}
templates_c = {}
templates_d = {}
templates_e = {}
templates_garki = {}
templates_new = {}
# reorder the templates so Vietnam 1st, Kenya 2nd, Solomon 3rd
for key in templates.keys():
if "Vietnam" in templates[key]["name"]:
templates_a.update({key: templates[key]})
for key in templates.keys():
if "Kenya" in templates[key]["name"]:
templates_b.update({key: templates[key]})
for key in templates.keys():
if "Solomon" in templates[key]["name"]:
templates_c.update({key: templates[key]})
for key in templates.keys():
if "Uganda" in templates[key]["name"]:
templates_d.update({key: templates[key]})
for key in templates.keys():
if "Bougainville" in templates[key]["name"]:
templates_e.update({key: templates[key]})
for key in templates.keys():
if "New Location" in templates[key]["name"]:
templates_new.update({key: templates[key]})
for key in templates.keys():
if "Garki" in templates[key]["name"]:
templates_garki.update({key: templates[key]})
pager_size = the_request.POST.get("pager_size")
if pager_size is None:
pager_size = 10
else:
pager_size = int(pager_size)
pager_offset = the_request.POST.get("pager_offset")
if pager_offset is None:
pager_offset = 0
else:
pager_offset = int(pager_offset)
pager_group = the_request.POST.get("pager_group")
if pager_group is None:
pager_group = 0
else:
try:
pager_group = int(pager_group)
except TypeError:
pager_group = 0
# scenario_count = scenarios.count()
template_count = len(templates)
pager_count = template_count / pager_size
if template_count % pager_size != 0:
pager_count += 1
context["pager_offset"] = pager_offset
context["pager_size"] = pager_size
context["pager_group"] = pager_group
context["pager_count"] = range(1, pager_count + 1)
context["pager_max"] = pager_count
context["templates_a"] = templates_a
context["templates_b"] = templates_b
context["templates_c"] = templates_c
context["templates_d"] = templates_d
context["templates_e"] = templates_e
context["templates_new"] = templates_new
context["templates_garki"] = templates_garki
context["template_count"] = template_count
context["current_start"] = pager_offset * pager_size + 1
context["current_stop"] = min(template_count, pager_offset * pager_size + pager_size)
return context
return context
def get_context_data(self, **kwargs):
"""Extension of get_context_data
Add context data to drive menu nav highlights and breadcrumbs.
"""
context = super(ScenarioDetailView, self).get_context_data(**kwargs)
context['nav_button'] = "browse_scenario"
self.request.session['emod_nav_button'] = "browse_scenario"
# This is here so that Alex can run this later and change all production database entries
# all_runs = DimRun.objects.all()
# for run in all_runs:
# if run.start_date_key and run.start_date_key.timestamp:
# run.new_start_date_key = run.start_date_key.timestamp
# if run.end_date_key and run.end_date_key.timestamp:
# run.new_end_date_key = run.end_date_key.timestamp
# print run.new_start_date_key
# print run.new_end_date_key
# run.save()
scenario_id = kwargs['scenario_id']
scenario = EMODBaseline.from_dw(pk=scenario_id)
# Hack until DimBaseline/EMODBaseline issues are sorted out
dim_scenario = DimBaseline.objects.get(id=scenario_id)
# Hack for calibration
species_info = {}
the_config = ast.literal_eval(scenario.get_config_file().content)
the_species = the_config['parameters']['Vector_Species_Params']
for specie in the_species:
species_info[specie] = {}
if 'EIR' in the_species[specie]:
eir = the_species[specie]['EIR']
else:
eir = 20.0 / float(len(the_species))
if 'Sporozoite_Rate' in the_species[specie]:
sporozoite = the_species[specie]['Sporozoite_Rate']
else:
sporozoite = 0.003
species_info[specie]['eir'] = eir
species_info[specie]['sporozoite'] = sporozoite
context['species_info'] = species_info
print species_info
# data_to_send = {}
# data_to_send['eir'] = []
# data_to_send['sporozoite'] = []
# the_config = ast.literal_eval(scenario.get_config_file().content)
# the_species = the_config['parameters']['Vector_Species_Params']
# for i in range(len(the_species)):
# data_to_send['eir'].append(20)
# data_to_send['sporozoite'].append(0.003)
# context['data_to_send'] = data_to_send
if dim_scenario.metadata and 'calibration_status' in dim_scenario.metadata:
scenario.calibration_status = json.loads(dim_scenario.metadata)['calibration_status']
else:
scenario.calibration_status = "Ready"
if dim_scenario.metadata:
current_metadata = json.loads(dim_scenario.metadata)
else:
current_metadata = {}
if 'calibration_verification_run_id' in current_metadata:
calibration_verification_run = DimRun.objects.get(id=current_metadata['calibration_verification_run_id'])
if calibration_verification_run.status == '1/1/0':
vector_species_parameters = the_config['parameters']['Vector_Species_Params']
calibration_verification_info = {}
for species in vector_species_parameters:
calibration_verification_info[species] = {}
calibration_verification_info[species]['sporozoite_rate'] = {}
calibration_verification_info[species]['eir'] = {}
calibration_verification_info[species]['biting_rate'] = {}
target_sporozoite_rate = vector_species_parameters[species]['Sporozoite_Rate']
daily_sporozoite_rate_2_3 = get_average_daily_sporozoite_rate(calibration_verification_run, species, 2, 3)
daily_sporozoite_rate_4_9 = get_average_daily_sporozoite_rate(calibration_verification_run, species, 4, 9)
daily_sporozoite_rate_10_20 = get_average_daily_sporozoite_rate(calibration_verification_run, species, 10, 20)
calibration_verification_info[species]['sporozoite_rate']['target'] = target_sporozoite_rate
calibration_verification_info[species]['sporozoite_rate']['years_2_3'] = daily_sporozoite_rate_2_3
calibration_verification_info[species]['sporozoite_rate']['years_4_9'] = daily_sporozoite_rate_4_9
calibration_verification_info[species]['sporozoite_rate']['years_10_20'] = daily_sporozoite_rate_10_20
target_average_annual_eir = vector_species_parameters[species]['EIR']
annual_eir_2_3 = get_average_daily_eir(calibration_verification_run, species, 2, 3) * 365
annual_eir_4_9 = get_average_daily_eir(calibration_verification_run, species, 4, 9) * 365
annual_eir_10_20 = get_average_daily_eir(calibration_verification_run, species, 10, 20) * 365
calibration_verification_info[species]['eir']['target'] = target_average_annual_eir
calibration_verification_info[species]['eir']['years_2_3'] = annual_eir_2_3
calibration_verification_info[species]['eir']['years_4_9'] = annual_eir_4_9
calibration_verification_info[species]['eir']['years_10_20'] = annual_eir_10_20
target_average_daily_biting_rate = 'NA'
daily_biting_rate_2_3 = get_average_daily_biting_rate(calibration_verification_run, species, 2, 3)
daily_biting_rate_4_9 = get_average_daily_biting_rate(calibration_verification_run, species, 4, 9)
daily_biting_rate_10_20 = get_average_daily_biting_rate(calibration_verification_run, species, 10, 20)
calibration_verification_info[species]['biting_rate']['target'] = target_average_daily_biting_rate
calibration_verification_info[species]['biting_rate']['years_2_3'] = daily_biting_rate_2_3
calibration_verification_info[species]['biting_rate']['years_4_9'] = daily_biting_rate_4_9
calibration_verification_info[species]['biting_rate']['years_10_20'] = daily_biting_rate_10_20
context['calibration_verification_info'] = calibration_verification_info
context['scenario_id'] = kwargs['scenario_id']
context['scenario_userid'] = scenario.user.id
context['dim_user'] = DimUser.objects.get_or_create(username=self.request.user.username)[0]
scenario.last_edited = scenario._last_edited
scenario.is_public = scenario._is_public
# Hack until DimBaseline/EMODBaseline issues are sorted out
if dim_scenario.metadata:
metadata = json.loads(dim_scenario.metadata)
if 'representative' in metadata:
scenario.is_representative = True
if 'is_complete' in metadata['representative']:
scenario.representative_is_completed = True
else:
scenario.representative_is_completed = False
scenario.name = derive_autoname(dim_scenario)
else:
scenario.is_representative = False
context['scenario'] = scenario
file_list = []
for my_file in scenario.files:
if my_file['type'] == 'config':
try:
context['config'] = json.dumps(ast.literal_eval(scenario.get_file_by_type('config').content),
sort_keys=True, indent=4, separators=(',', ': '))
except AttributeError:
# if file list was returned, use last file
context['config'] = json.dumps(ast.literal_eval(
scenario.get_file_by_type('config')[scenario.get_file_by_type('config').count()
- 1].content), sort_keys=True, indent=4,
separators=(',', ': '))
elif my_file['type'] == 'campaign':
try:
scenario_campaign = json.dumps(ast.literal_eval(scenario.get_file_by_type('campaign').content),
sort_keys=True, indent=4, separators=(',', ': '))
if len(json.loads(scenario_campaign)['Events']) > 0:
context['campaign'] = scenario_campaign
else:
context['has_campaign'] = None
except AttributeError:
# if file list was returned, use last file
context['campaign'] = json.dumps(ast.literal_eval(
scenario.get_file_by_type('campaign')[scenario.get_file_by_type('campaign').count()
- 1].content), sort_keys=True, indent=4,
separators=(',', ': '))
else:
file_list.append(my_file['name'])
context['file_list'] = file_list
# Get a list of the runs for this scenario
adapter = EMOD_Adapter(self.request.user.username)
run_list = DimRun.objects.filter(baseline_key=scenario.id)
dim_scenario = DimBaseline.objects.get(id=scenario.id)
if dim_scenario.simulation_group:
simulation_group = dim_scenario.simulation_group
simulation_list = Simulation.objects.filter(group=simulation_group)
for simulation in simulation_list:
if simulation.status == sim_status.SCRIPT_DONE:
simulation.is_complete = True
elif simulation.status == sim_status.SCRIPT_ERROR:
simulation.has_failed = True
context['simulation_list'] = simulation_list
# sort descending by id (for those old runs that all have the same old time_created
context['run_list'] = sorted(run_list, key=lambda x: x.id, reverse=True)
# sort descending by time_saved
context['run_list'] = sorted(context['run_list'], key=lambda x: x.time_created, reverse=True)
note_list = []
for run in context['run_list']:
try:
run_diffs = []
# config diffs
run_config = run.jcd.jcdict['config.json']['Changes'][0]['config.json/parameters']
scenario_config = json.loads(context['config'])['parameters']
for key in scenario_config:
if scenario_config[key] != run_config[key]:
run_diffs.append({'key': key, 'run': run_config[key], 'scenario': scenario_config[key]})
# ToDo: split out each key difference of Vector Species Parameters in both
# campaign diffs
if 'campaign.json' not in run.jcd.jcdict:
run_diffs.append({'key': 'Interventions', 'run': 'None'})
else:
run_campaign = run.jcd.jcdict['campaign.json']['Changes'][0]['campaign.json/Events']
if json.loads(scenario_campaign)['Events'] != run_campaign:
run_diffs.append({'key': 'Interventions', 'run': run_campaign,
'scenario': str(json.loads(scenario_campaign)['Events'])})
# ToDo: split out each key difference of each Intervention in both
# else:
# run_diffs.append({'key': 'Interventions', 'run': 'See below',
# 'scenario': '<a class="btn tooltip_link" href="#campaign">see below</a>'})
run.diffs = run_diffs
except (AttributeError, KeyError):
# no JCD?
run.diffs = [{'Unknown Error Occurred:': 'no changes found.'}]
# get the status of each run
status = adapter.run_status(run.id)
if status is None:
run.my_completed = None
else:
run.my_completed = status[0]
run.my_total = status[1]
run.my_failed = status[2]
run.percent_complete = (run.my_completed + run.my_failed) / run.my_total
run.my_incomplete = int(run.my_total) - (int(run.my_completed) + int(run.my_failed))
if int(status[0]) > 0:
context['has_results'] = 1
note_list.extend(adapter.fetch_notes(run_id=int(run.id), as_object=True))
if note_list != []:
context['note_list'] = note_list
return context
def get_context_data(self, **kwargs):
"""Extension of get_context_data
Add context data to drive menu nav highlights, breadcrumbs and pagers.
"""
context = super(ScenarioBrowsePublicView, self).get_context_data(**kwargs)
the_request = self.request
context['nav_button'] = 'scenario_browse_public'
if context['object_list'] is None:
return context
pager_size = the_request.POST.get('pager_size') or the_request.GET.get('pager_size')
if pager_size is None:
pager_size = 10
else:
pager_size = int(pager_size)
paginator = Paginator(context['object_list'], pager_size)
page = int(the_request.GET.get('page') or 1)
try:
scenario_list = paginator.page(page)
except PageNotAnInteger:
# If page is not an integer, deliver first page.
scenario_list = paginator.page(1)
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
scenario_list = paginator.page(paginator.num_pages)
scenario_count = paginator.count
context['pager_size'] = pager_size
context['scenario_list'] = scenario_list.object_list
context['pager_obj'] = scenario_list
context['scenario_range'] = range(paginator.num_pages)
context['scenario_count'] = scenario_count
context['current_start'] = (page-1)*pager_size + 1
context['current_stop'] = min(scenario_count, (page-1)*pager_size + pager_size)
context['dim_user'] = DimUser.objects.get_or_create(username=self.request.user.username)[0]
adapter = EMOD_Adapter(self.request.user.username)
for scenario in context['scenario_list']:
run_list = DimRun.objects.filter(baseline_key=scenario.id).order_by('-id')
scenario.run_list = run_list
scenario.run_count = len(run_list)
scenario.run_id = 0 # set a dummy id
my_model_version = ''
# get status for each run
for run in run_list:
status = adapter.run_status(run.id)
if status is None:
run.my_completed = "No"
else:
run.my_completed = status[0]
run.my_failed = status[2]
if int(status[0]) > 0:
scenario.run_id = run.id
scenario.run_name = run.name
scenario.location_key = run.location_key
#break
my_model_version = run.model_version
try:
scenario.model_version = scenario.my_scenario.my_model_version
except (AttributeError, ObjectDoesNotExist):
scenario.model_version = my_model_version
return context