def submitsdm(self):
# TODO: catch UNAuthorized correctly and return json error
if self.request.get('REQUEST_METHOD', 'GET').upper() != 'POST':
self.record_error('Request must be POST', 400)
raise BadRequest('Request must be POST')
# make sure we have the right context
if ISiteRoot.providedBy(self.context):
# we have been called at site root... let's traverse to default
# experiments location
context = self.context.restrictedTraverse(
defaults.EXPERIMENTS_FOLDER_ID)
else:
# custom context.... let's use in
context = self.context
# parse request body
params = self.request.form
# validate input
# TODO: should validate type as well..... (e.g. string has to be
# string)
# TODO: validate dataset and layer id's existence if possible
props = {}
if not params.get('title', None):
self.record_error('Bad Request', 400, 'Missing parameter title',
{'parameter': 'title'})
else:
props['title'] = params['title']
props['description'] = params.get('description', '')
if not params.get('occurrence_data', None):
self.record_error('Bad Request', 400,
'Missing parameter occurrence_data',
{'parameter': 'occurrence_data'})
else:
# FIXME: should properly support source / id
# for now only bccvl source is supported
props['species_occurrence_dataset'] = params[
'occurrence_data']['id']
# FIXME: should properly support source/id for onw only bccvl source is
# supported
props['species_absence_dataset'] = params.get(
'absence_data', {}).get('id', None)
props['scale_down'] = params.get('scale_down', False)
if not params.get('environmental_data', None):
self.record_error('Bad Request', 400,
'Missing parameter environmental_data',
{'parameter': 'environmental_data'})
else:
props['environmental_datasets'] = params['environmental_data']
if params.get('modelling_region', ''):
props['modelling_region'] = NamedBlobFile(
data=json.dumps(params['modelling_region']))
else:
props['modelling_region'] = None
if not params.get('algorithms', None):
self.record_error('Bad Request', 400,
'Missing parameter algorithms',
{'parameter': 'algorithms'})
else:
portal = ploneapi.portal.get()
props['functions'] = {}
# FIXME: make sure we get the default values from our func object
for algo, algo_params in params['algorithms'].items():
if algo_params is None:
algo_params = {}
toolkit = portal[defaults.FUNCTIONS_FOLDER_ID][algo]
toolkit_model = loadString(toolkit.schema)
toolkit_schema = toolkit_model.schema
func_props = {}
for field_name in toolkit_schema.names():
field = toolkit_schema.get(field_name)
value = algo_params.get(field_name, field.missing_value)
if value == field.missing_value:
func_props[field_name] = field.default
else:
func_props[field_name] = value
props['functions'][IUUID(toolkit)] = func_props
if self.errors:
raise BadRequest("Validation Failed")
# create experiment with data as form would do
# TODO: make sure self.context is 'experiments' folder?
from plone.dexterity.utils import createContent, addContentToContainer
experiment = createContent("org.bccvl.content.sdmexperiment", **props)
experiment = addContentToContainer(context, experiment)
# TODO: check if props and algo params have been applied properly
experiment.parameters = dict(props['functions'])
# FIXME: need to get resolution from somewhere
IBCCVLMetadata(experiment)['resolution'] = 'Resolution30m'
# submit newly created experiment
# TODO: handle background job submit .... at this stage we wouldn't
# know the model run job ids
# TODO: handle submit errors and other errors that may happen above?
# generic exceptions could behandled in returnwrapper
retval = {
'experiment': {
'url': experiment.absolute_url(),
'uuid': IUUID(experiment)
},
'jobs': [],
}
jt = IExperimentJobTracker(experiment)
msgtype, msg = jt.start_job(self.request)
if msgtype is not None:
retval['message'] = {
'type': msgtype,
'message': msg
}
for result in experiment.values():
jt = IJobTracker(result)
retval['jobs'].append(jt.get_job().id)
return retval
def submittraits(self):
# TODO: catch UNAuthorized correctly and return json error
if self.request.get('REQUEST_METHOD', 'GET').upper() != 'POST':
self.record_error('Request must be POST', 400)
raise BadRequest('Request must be POST')
# make sure we have the right context
if ISiteRoot.providedBy(self.context):
# we have been called at site root... let's traverse to default
# experiments location
context = self.context.restrictedTraverse(
defaults.EXPERIMENTS_FOLDER_ID)
else:
# custom context.... let's use in
context = self.context
# parse request body
params = self.request.form
# validate input
# TODO: should validate type as well..... (e.g. string has to be
# string)
# TODO: validate dataset and layer id's existence if possible
props = {}
if params.get('species_list', None):
props['species_list'] = params['species_list']
else:
self.record_error('Bad Request', 400, 'Missing parameter speciesList',
{'parameter': 'speciesList'})
if not params.get('title', None):
self.record_error('Bad Request', 400, 'Missing parameter title',
{'parameter': 'title'})
else:
props['title'] = params['title']
props['description'] = params.get('description', '')
if not params.get('traits_data', None):
self.record_error('Bad Request', 400,
'Missing parameter traits_data',
{'parameter': 'traits_data'})
else:
# FIXME: should properly support source / id
# for now only bccvl source is supported
props['species_traits_dataset'] = params[
'traits_data']['id']
props['species_traits_dataset_params'] = {}
for col_name, col_val in params.get("columns", {}).items():
if col_val not in ('lat', 'lon', 'species', 'trait_con',
'trait_ord', 'trait_nom', 'env_var_con',
'env_var_cat', 'random_con', 'random_cat'):
continue
props['species_traits_dataset_params'][col_name] = col_val
if not props['species_traits_dataset_params']:
self.record_error('Bad Request', 400,
'Invalid values for columns',
{'parameter': 'columns'})
# Check for species-level trait data i.e. species is not specified
if 'species' not in props['species_traits_dataset_params'].values():
props['species_list'] = []
props['scale_down'] = params.get('scale_down', False)
# env data is optional
props['environmental_datasets'] = params.get('environmental_data', None)
if not (props['environmental_datasets']
or 'env_var_con' not in props['species_traits_dataset_params'].values()
or 'env_var_cat' not in props['species_traits_dataset_params'].values()):
self.record_error('Bad Request', 400,
'No Environmental data selected',
{'parameter': 'environmental_datasets'})
if params.get('modelling_region', ''):
props['modelling_region'] = NamedBlobFile(
data=json.dumps(params['modelling_region']))
else:
props['modelling_region'] = None
if not params.get('algorithms', None):
self.record_error('Bad Request', 400,
'Missing parameter algorithms',
{'parameter': 'algorithms'})
else:
props['algorithms_species'] = {}
props['algorithms_diff'] = {}
funcs_env = getUtility(
IVocabularyFactory, 'traits_functions_species_source')(context)
funcs_species = getUtility(
IVocabularyFactory, 'traits_functions_diff_source')(context)
# FIXME: make sure we get the default values from our func object
for algo_uuid, algo_params in params['algorithms'].items():
if algo_params is None:
algo_params = {}
toolkit = uuidToObject(algo_uuid)
toolkit_model = loadString(toolkit.schema)
toolkit_schema = toolkit_model.schema
func_props = {}
for field_name in toolkit_schema.names():
field = toolkit_schema.get(field_name)
value = algo_params.get(field_name, field.missing_value)
if value == field.missing_value:
func_props[field_name] = field.default
else:
func_props[field_name] = value
if algo_uuid in funcs_env:
props['algorithms_species'][algo_uuid] = func_props
elif algo_uuid in funcs_species:
props['algorithms_diff'][algo_uuid] = func_props
else:
LOG.warn(
'Algorithm {} not in allowed list of functions'.format(toolkit.id))
if not (props['algorithms_species'] or props['algorithms_diff']):
self.record_error('Bad Request', 400,
'Iinvalid algorithms selected',
{'parameter': 'algorithms'})
if self.errors:
raise BadRequest("Validation Failed")
# create experiment with data as form would do
# TODO: make sure self.context is 'experiments' folder?
from plone.dexterity.utils import createContent, addContentToContainer
experiment = createContent(
"org.bccvl.content.speciestraitsexperiment", **props)
experiment = addContentToContainer(context, experiment)
experiment.parameters = dict(props['algorithms_species'])
experiment.parameters.update(dict(props['algorithms_diff']))
# FIXME: need to get resolution from somewhere
IBCCVLMetadata(experiment)['resolution'] = 'Resolution30m'
# submit newly created experiment
# TODO: handle background job submit .... at this stage we wouldn't
# know the model run job ids
# TODO: handle submit errors and other errors that may happen above?
# generic exceptions could behandled in returnwrapper
retval = {
'experiment': {
'url': experiment.absolute_url(),
'uuid': IUUID(experiment)
},
'jobs': [],
}
jt = IExperimentJobTracker(experiment)
msgtype, msg = jt.start_job(self.request)
if msgtype is not None:
retval['message'] = {
'type': msgtype,
'message': msg
}
for result in experiment.values():
jt = IJobTracker(result)
retval['jobs'].append(jt.get_job().id)
return retval
def submitcc(self):
# TODO: catch UNAuthorized correctly and return json error
if self.request.get('REQUEST_METHOD', 'GET').upper() != 'POST':
self.record_error('Request must be POST', 400)
raise BadRequest('Request must be POST')
# make sure we have the right context
if ISiteRoot.providedBy(self.context):
# we have been called at site root... let's traverse to default
# experiments location
context = self.context.restrictedTraverse(
defaults.EXPERIMENTS_FOLDER_ID)
else:
# custom context.... let's use in
context = self.context
# parse request body
params = self.request.form
# validate input
# TODO: should validate type as well..... (e.g. string has to be
# string)
# TODO: validate dataset and layer id's existence if possible
props = {}
if not params.get('title', None):
self.record_error('Bad Request', 400, 'Missing parameter title',
{'parameter': 'title'})
else:
props['title'] = params['title']
props['description'] = params.get('description', '')
if not params.get('species_distribution_models', None):
self.record_error('Bad Request', 400,
'Missing parameter species_distribution_models',
{'parameter': 'species_distribution_models'})
else:
props['species_distribution_models'] = params[
'species_distribution_models']
if not params.get('future_climate_datasets', None):
self.record_error('Bad Request', 400,
'Missing parameter future_climate_datasets',
{'parameter': 'future_climate_datasets'})
else:
props['future_climate_datasets'] = params[
'future_climate_datasets']
if params.get('projection_region', ''):
props['projection_region'] = NamedBlobFile(
data=json.dumps(params['projection_region']))
else:
props['projection_region'] = None
if self.errors:
raise BadRequest("Validation Failed")
# create experiment with data as form would do
# TODO: make sure self.context is 'experiments' folder?
from plone.dexterity.utils import createContent, addContentToContainer
experiment = createContent("org.bccvl.content.projectionexperiment",
**props)
experiment = addContentToContainer(context, experiment)
# FIXME: need to get resolution from somewhere
IBCCVLMetadata(experiment)['resolution'] = 'Resolution30m'
# submit newly created experiment
# TODO: handle background job submit .... at this stage we wouldn't
# know the model run job ids
# TODO: handle submit errors and other errors that may happen above?
# generic exceptions could behandled in returnwrapper
retval = {
'experiment': {
'url': experiment.absolute_url(),
'uuid': IUUID(experiment)
},
'jobs': [],
}
jt = IExperimentJobTracker(experiment)
msgtype, msg = jt.start_job(self.request)
if msgtype is not None:
retval['message'] = {
'type': msgtype,
'message': msg
}
for result in experiment.values():
jt = IJobTracker(result)
retval['jobs'].append(jt.get_job().id)
return retval
def submitsdm(self):
# TODO: catch UNAuthorized correctly and return json error
if self.request.get('REQUEST_METHOD', 'GET').upper() != 'POST':
self.record_error('Request must be POST', 400)
raise BadRequest('Request must be POST')
# make sure we have the right context
if ISiteRoot.providedBy(self.context):
# we have been called at site root... let's traverse to default
# experiments location
context = self.context.restrictedTraverse(
defaults.EXPERIMENTS_FOLDER_ID)
else:
# custom context.... let's use in
context = self.context
# parse request body
params = self.request.form
# validate input
# TODO: should validate type as well..... (e.g. string has to be
# string)
# TODO: validate dataset and layer id's existence if possible
props = {}
if not params.get('title', None):
self.record_error('Bad Request', 400, 'Missing parameter title',
{'parameter': 'title'})
else:
props['title'] = params['title']
props['description'] = params.get('description', '')
if not params.get('occurrence_data', None):
self.record_error('Bad Request', 400,
'Missing parameter occurrence_data',
{'parameter': 'occurrence_data'})
else:
# FIXME: should properly support source / id
# for now only bccvl source is supported
props['species_occurrence_dataset'] = params[
'occurrence_data']['id']
# FIXME: should properly support source/id for onw only bccvl source is
# supported
props['species_absence_dataset'] = params.get(
'absence_data', {}).get('id', None)
props['scale_down'] = params.get('scale_down', False)
if not params.get('environmental_data', None):
self.record_error('Bad Request', 400,
'Missing parameter environmental_data',
{'parameter': 'environmental_data'})
else:
props['environmental_datasets'] = params['environmental_data']
if params.get('modelling_region', ''):
props['modelling_region'] = NamedBlobFile(
data=json.dumps(params['modelling_region']))
else:
props['modelling_region'] = None
if not params.get('algorithms', None):
self.record_error('Bad Request', 400,
'Missing parameter algorithms',
{'parameter': 'algorithms'})
else:
portal = ploneapi.portal.get()
props['functions'] = {}
# FIXME: make sure we get the default values from our func object
for algo, algo_params in params['algorithms'].items():
if algo_params is None:
algo_params = {}
toolkit = portal[defaults.FUNCTIONS_FOLDER_ID][algo]
toolkit_model = loadString(toolkit.schema)
toolkit_schema = toolkit_model.schema
func_props = {}
for field_name in toolkit_schema.names():
field = toolkit_schema.get(field_name)
value = algo_params.get(field_name, field.missing_value)
if value == field.missing_value:
func_props[field_name] = field.default
else:
func_props[field_name] = value
props['functions'][IUUID(toolkit)] = func_props
if self.errors:
raise BadRequest("Validation Failed")
# create experiment with data as form would do
# TODO: make sure self.context is 'experiments' folder?
from plone.dexterity.utils import createContent, addContentToContainer
experiment = createContent("org.bccvl.content.sdmexperiment", **props)
experiment = addContentToContainer(context, experiment)
# TODO: check if props and algo params have been applied properly
experiment.parameters = dict(props['functions'])
# FIXME: need to get resolution from somewhere
IBCCVLMetadata(experiment)['resolution'] = 'Resolution30m'
# submit newly created experiment
# TODO: handle background job submit .... at this stage we wouldn't
# know the model run job ids
# TODO: handle submit errors and other errors that may happen above?
# generic exceptions could behandled in returnwrapper
retval = {
'experiment': {
'url': experiment.absolute_url(),
'uuid': IUUID(experiment)
},
'jobs': [],
}
jt = IExperimentJobTracker(experiment)
msgtype, msg = jt.start_job(self.request)
if msgtype is not None:
retval['message'] = {
'type': msgtype,
'message': msg
}
for result in experiment.values():
jt = IJobTracker(result)
retval['jobs'].append(jt.get_job().id)
return retval
def submittraits(self):
# TODO: catch UNAuthorized correctly and return json error
if self.request.get('REQUEST_METHOD', 'GET').upper() != 'POST':
self.record_error('Request must be POST', 400)
raise BadRequest('Request must be POST')
# make sure we have the right context
if ISiteRoot.providedBy(self.context):
# we have been called at site root... let's traverse to default
# experiments location
context = self.context.restrictedTraverse(
defaults.EXPERIMENTS_FOLDER_ID)
else:
# custom context.... let's use in
context = self.context
# parse request body
params = self.request.form
# validate input
# TODO: should validate type as well..... (e.g. string has to be
# string)
# TODO: validate dataset and layer id's existence if possible
props = {}
if params.get('species_list', None):
props['species_list'] = params['species_list']
else:
self.record_error('Bad Request', 400, 'Missing parameter speciesList',
{'parameter': 'speciesList'})
if not params.get('title', None):
self.record_error('Bad Request', 400, 'Missing parameter title',
{'parameter': 'title'})
else:
props['title'] = params['title']
props['description'] = params.get('description', '')
if not params.get('traits_data', None):
self.record_error('Bad Request', 400,
'Missing parameter traits_data',
{'parameter': 'traits_data'})
else:
# FIXME: should properly support source / id
# for now only bccvl source is supported
props['species_traits_dataset'] = params[
'traits_data']['id']
props['species_traits_dataset_params'] = {}
for col_name, col_val in params.get("columns", {}).items():
if col_val not in ('lat', 'lon', 'species', 'trait_con',
'trait_ord', 'trait_nom', 'env_var_con',
'env_var_cat', 'random_con', 'random_cat'):
continue
props['species_traits_dataset_params'][col_name] = col_val
if not props['species_traits_dataset_params']:
self.record_error('Bad Request', 400,
'Invalid values for columns',
{'parameter': 'columns'})
# Check for species-level trait data i.e. species is not specified
if 'species' not in props['species_traits_dataset_params'].values():
props['species_list'] = []
props['scale_down'] = params.get('scale_down', False)
# env data is optional
props['environmental_datasets'] = params.get('environmental_data', None)
if not (props['environmental_datasets']
or 'env_var_con' not in props['species_traits_dataset_params'].values()
or 'env_var_cat' not in props['species_traits_dataset_params'].values()):
self.record_error('Bad Request', 400,
'No Environmental data selected',
{'parameter': 'environmental_datasets'})
if params.get('modelling_region', ''):
props['modelling_region'] = NamedBlobFile(
data=json.dumps(params['modelling_region']))
else:
props['modelling_region'] = None
if not params.get('algorithms', None):
self.record_error('Bad Request', 400,
'Missing parameter algorithms',
{'parameter': 'algorithms'})
else:
props['algorithms_species'] = {}
props['algorithms_diff'] = {}
funcs_env = getUtility(
IVocabularyFactory, 'traits_functions_species_source')(context)
funcs_species = getUtility(
IVocabularyFactory, 'traits_functions_diff_source')(context)
# FIXME: make sure we get the default values from our func object
for algo_uuid, algo_params in params['algorithms'].items():
if algo_params is None:
algo_params = {}
toolkit = uuidToObject(algo_uuid)
toolkit_model = loadString(toolkit.schema)
toolkit_schema = toolkit_model.schema
func_props = {}
for field_name in toolkit_schema.names():
field = toolkit_schema.get(field_name)
value = algo_params.get(field_name, field.missing_value)
if value == field.missing_value:
func_props[field_name] = field.default
else:
func_props[field_name] = value
if algo_uuid in funcs_env:
props['algorithms_species'][algo_uuid] = func_props
elif algo_uuid in funcs_species:
props['algorithms_diff'][algo_uuid] = func_props
else:
LOG.warn(
'Algorithm {} not in allowed list of functions'.format(toolkit.id))
if not (props['algorithms_species'] or props['algorithms_diff']):
self.record_error('Bad Request', 400,
'Iinvalid algorithms selected',
{'parameter': 'algorithms'})
if self.errors:
raise BadRequest("Validation Failed")
# create experiment with data as form would do
# TODO: make sure self.context is 'experiments' folder?
from plone.dexterity.utils import createContent, addContentToContainer
experiment = createContent(
"org.bccvl.content.speciestraitsexperiment", **props)
experiment = addContentToContainer(context, experiment)
experiment.parameters = dict(props['algorithms_species'])
experiment.parameters.update(dict(props['algorithms_diff']))
# FIXME: need to get resolution from somewhere
IBCCVLMetadata(experiment)['resolution'] = 'Resolution30m'
# submit newly created experiment
# TODO: handle background job submit .... at this stage we wouldn't
# know the model run job ids
# TODO: handle submit errors and other errors that may happen above?
# generic exceptions could behandled in returnwrapper
retval = {
'experiment': {
'url': experiment.absolute_url(),
'uuid': IUUID(experiment)
},
'jobs': [],
}
jt = IExperimentJobTracker(experiment)
msgtype, msg = jt.start_job(self.request)
if msgtype is not None:
retval['message'] = {
'type': msgtype,
'message': msg
}
for result in experiment.values():
jt = IJobTracker(result)
retval['jobs'].append(jt.get_job().id)
return retval
def submitcc(self):
# TODO: catch UNAuthorized correctly and return json error
if self.request.get('REQUEST_METHOD', 'GET').upper() != 'POST':
self.record_error('Request must be POST', 400)
raise BadRequest('Request must be POST')
# make sure we have the right context
if ISiteRoot.providedBy(self.context):
# we have been called at site root... let's traverse to default
# experiments location
context = self.context.restrictedTraverse(
defaults.EXPERIMENTS_FOLDER_ID)
else:
# custom context.... let's use in
context = self.context
# parse request body
params = self.request.form
# validate input
# TODO: should validate type as well..... (e.g. string has to be
# string)
# TODO: validate dataset and layer id's existence if possible
props = {}
if not params.get('title', None):
self.record_error('Bad Request', 400, 'Missing parameter title',
{'parameter': 'title'})
else:
props['title'] = params['title']
props['description'] = params.get('description', '')
if not params.get('species_distribution_models', None):
self.record_error('Bad Request', 400,
'Missing parameter species_distribution_models',
{'parameter': 'species_distribution_models'})
else:
props['species_distribution_models'] = params[
'species_distribution_models']
if not params.get('future_climate_datasets', None):
self.record_error('Bad Request', 400,
'Missing parameter future_climate_datasets',
{'parameter': 'future_climate_datasets'})
else:
props['future_climate_datasets'] = params[
'future_climate_datasets']
if params.get('projection_region', ''):
props['projection_region'] = NamedBlobFile(
data=json.dumps(params['projection_region']))
else:
props['projection_region'] = None
if self.errors:
raise BadRequest("Validation Failed")
# create experiment with data as form would do
# TODO: make sure self.context is 'experiments' folder?
from plone.dexterity.utils import createContent, addContentToContainer
experiment = createContent("org.bccvl.content.projectionexperiment",
**props)
experiment = addContentToContainer(context, experiment)
# FIXME: need to get resolution from somewhere
IBCCVLMetadata(experiment)['resolution'] = 'Resolution30m'
# submit newly created experiment
# TODO: handle background job submit .... at this stage we wouldn't
# know the model run job ids
# TODO: handle submit errors and other errors that may happen above?
# generic exceptions could behandled in returnwrapper
retval = {
'experiment': {
'url': experiment.absolute_url(),
'uuid': IUUID(experiment)
},
'jobs': [],
}
jt = IExperimentJobTracker(experiment)
msgtype, msg = jt.start_job(self.request)
if msgtype is not None:
retval['message'] = {
'type': msgtype,
'message': msg
}
for result in experiment.values():
jt = IJobTracker(result)
retval['jobs'].append(jt.get_job().id)
return retval
