def connector_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different processing functions
"""
command_args, _, api, session_file, _ = get_context(args, SETTINGS)
path = u.check_dir(command_args.output)
log = None
if command_args.log_file:
u.check_dir(command_args.log_file)
log = command_args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
if not command_args.external_connector_id and \
u.has_connection_info(command_args):
# create connector
pec.connector_processing(api,
command_args,
command_args.resume,
session_file=session_file,
path=path,
log=log)
if command_args.external_connector_id and (
command_args.connector_attributes or command_args.name
or command_args.tag or command_args.description
or command_args.category):
# update connector's attributes
pec.update_external_connector(command_args, api, command_args.resume, \
session_file=session_file)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir,
log_file=session_file,
verbosity=command_args.verbosity)
def reify_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different processing functions
"""
# If --clear-logs the log files are cleared
if "--clear-logs" in args:
clear_log_files(LOG_FILES)
command_args, command, api, session_file, resume = get_context(args,
SETTINGS)
def logger(message):
"""Partial to log messages according to args.verbosity
"""
u.log_message(u.dated(message), \
log_file=session_file, console=command_args.verbosity)
print command_args.output, command_args.output_dir
message = "Starting reification for %s\n\n" % command_args.resource_id
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
reify_resources(command_args, api, logger)
message = "\nReification complete. See the results in %s\n\n" % \
command_args.output
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir, log_file=session_file,
verbosity=command_args.verbosity)
def project_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different processing functions
"""
command_args, command, api, session_file, resume = get_context(args,
SETTINGS)
path = u.check_dir(command_args.output)
log = None
if command_args.log_file:
u.check_dir(command_args.log_file)
log = command_args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
if not command_args.project_id and command_args.name:
command_args.project = command_args.name
if command_args.project:
# create project
pp.project_processing(
api, command_args, command_args.resume, session_file=session_file,
path=path, log=log, create=True)
if command_args.project_id and (
command_args.project_attributes or
command_args.name or command_args.tag or command_args.description
or command_args.category):
# update project's attributes
pp.update_project(command_args, api, command_args.resume, \
session_file=session_file)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir, log_file=session_file,
verbosity=command_args.verbosity)
def reify_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different processing functions
"""
# If --clear-logs the log files are cleared
if "--clear-logs" in args:
clear_log_files(LOG_FILES)
command_args, _, api, session_file, _ = get_context(args, SETTINGS)
def logger(message):
"""Partial to log messages according to args.verbosity
"""
u.log_message(u.dated(message), \
log_file=session_file, console=command_args.verbosity)
message = "Starting reification for %s\n\n" % command_args.resource_id
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
reify_resources(command_args, api)
message = "\nReification complete. See the results in %s\n\n" % \
command_args.output
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir,
log_file=session_file,
verbosity=command_args.verbosity)
def project_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different processing functions
"""
command_args, command, api, session_file, resume = get_context(args,
SETTINGS)
path = u.check_dir(command_args.output)
log = None
if command_args.log_file:
u.check_dir(command_args.log_file)
log = command_args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
if not command_args.project_id and command_args.name:
command_args.project = command_args.name
if command_args.project:
# create project
pp.project_processing(
api, command_args, command_args.resume, session_file=session_file,
path=path, log=log, create=True)
if command_args.project_id and (
command_args.project_attributes or
command_args.name or command_args.tag or command_args.description
or command_args.category):
# update project's attributes
pp.update_project(command_args, api, command_args.resume, \
session_file=session_file)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir, log_file=session_file,
verbosity=command_args.verbosity)
def execute_whizzml(args, api, session_file):
"""executes the code in a script or a source code file
"""
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
path = args.output_dir
if args.to_library:
library = pw.library_processing(api,
args,
session_file=session_file,
path=path,
log=log)
else:
if args.script_file:
# script is retrieved from the contents of the given local JSON file
script, _, _ = u.read_local_resource(args.script_file)
args.script = script['resource']
args.script_ids = [args.script]
elif args.code_file or args.code:
script, scripts = pw.script_processing(api,
args,
session_file=session_file,
path=path,
log=log)
args.script = script['resource']
args.script_ids = scripts
if (args.script or args.scripts) and not args.no_execute:
execution = pw.execution_processing(api,
args,
session_file=session_file,
path=path,
log=log)
execution = r.get_execution( \
execution, api, args.verbosity, session_file)
r.save_txt_and_json(execution['object']['execution'],
args.output,
api=api)
args.execution = execution['resource']
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(args.output_dir,
log_file=session_file,
verbosity=args.verbosity)
def execute_whizzml(args, api, session_file):
"""executes the code in a script or a source code file
"""
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
path = args.output_dir
if args.to_library:
pw.library_processing( \
api, args, session_file=session_file, path=path, log=log)
else:
if args.script_file:
# script is retrieved from the contents of the given local file
script, _, _ = u.read_local_resource(args.script_file)
args.script = script['resource']
args.script_ids = [args.script]
elif args.code_file or args.code:
script, scripts = pw.script_processing( \
api, args, session_file=session_file, path=path, log=log)
args.script = script if isinstance(script, basestring) else \
script.get('resource')
args.script_ids = scripts
if (args.script or args.scripts) and not args.no_execute:
execution = pw.execution_processing( \
api, args, session_file=session_file, path=path, log=log)
execution = r.get_execution( \
execution, api, args.verbosity, session_file)
r.save_txt_and_json(execution['object']['execution'],
args.output, api=api)
args.execution = execution['resource']
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(args.output_dir, log_file=session_file,
verbosity=args.verbosity)
def export_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different export functions
"""
# If --clear-logs the log files are cleared
if "--clear-logs" in args:
clear_log_files(LOG_FILES)
command_args, command, api, session_file, resume = get_context(args,
SETTINGS)
# Creates the corresponding api instance
resource = command_args.ensemble or command_args.model
message = "Generating %s code for %s\n\n" % (command_args.language,
resource)
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
export_code(command_args, api)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir, log_file=session_file,
verbosity=command_args.verbosity)
def export_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different export functions
"""
# If --clear-logs the log files are cleared
if "--clear-logs" in args:
clear_log_files(LOG_FILES)
command_args, _, api, session_file, _ = get_context(args, SETTINGS)
# Creates the corresponding api instance
resource = command_args.ensemble or command_args.model
message = "Generating %s code for %s\n\n" % (command_args.language,
resource)
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
export_code(command_args, api)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir,
log_file=session_file,
verbosity=command_args.verbosity)
def compute_output(api, args):
""" Creates a dataset using the `training_set`.
"""
source = None
dataset = None
fields = None
other_label = OTHER
multi_label_data = None
multi_label_fields = []
datasets = None
# variables from command-line options
resume = args.resume_
output = args.output
dataset_fields = args.dataset_fields_
check_args_coherence(args)
path = u.check_dir(output)
session_file = "%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# labels to be used in multi-label expansion
labels = (None if args.labels is None else
[label.strip() for label in
args.labels.split(args.args_separator)])
if labels is not None:
labels = sorted([label for label in labels])
# multi_label file must be preprocessed to obtain a new extended file
if args.multi_label and args.training_set is not None:
(args.training_set, multi_label_data) = ps.multi_label_expansion(
args.training_set, args.train_header, args, path,
labels=labels, session_file=session_file)
args.train_header = True
args.objective_field = multi_label_data["objective_name"]
all_labels = l.get_all_labels(multi_label_data)
if not labels:
labels = all_labels
else:
all_labels = labels
if args.objective_field:
csv_properties.update({'objective_field': args.objective_field})
if args.source_file:
# source is retrieved from the contents of the given local JSON file
source, csv_properties, fields = u.read_local_resource(
args.source_file,
csv_properties=csv_properties)
else:
# source is retrieved from the remote object
source, resume, csv_properties, fields = ps.source_processing(
api, args, resume,
csv_properties=csv_properties, multi_label_data=multi_label_data,
session_file=session_file, path=path, log=log)
if source is not None:
args.source = bigml.api.get_source_id(source)
if args.multi_label and source:
multi_label_data = l.get_multi_label_data(source)
(args.objective_field,
labels,
all_labels,
multi_label_fields) = l.multi_label_sync(args.objective_field,
labels,
multi_label_data,
fields,
multi_label_fields)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
if args.dataset_file:
# dataset is retrieved from the contents of the given local JSON file
model_dataset, csv_properties, fields = u.read_local_resource(
args.dataset_file,
csv_properties=csv_properties)
if not args.datasets:
datasets = [model_dataset]
dataset = model_dataset
else:
datasets = u.read_datasets(args.datasets)
if not datasets:
# dataset is retrieved from the remote object
datasets, resume, csv_properties, fields = pd.dataset_processing(
source, api, args, resume,
fields=fields,
csv_properties=csv_properties,
multi_label_data=multi_label_data,
session_file=session_file, path=path, log=log)
if datasets:
dataset = datasets[-1]
if args.to_csv is not None:
resume = pd.export_dataset(dataset, api, args, resume,
session_file=session_file, path=path)
# Now we have a dataset, let's check if there's an objective_field
# given by the user and update it in the fields structure
args.objective_id_ = get_objective_id(args, fields)
# If test_split is used, split the dataset in a training and a test dataset
# according to the given split
if args.test_split > 0:
dataset, test_dataset, resume = pd.split_processing(
dataset, api, args, resume,
multi_label_data=multi_label_data,
session_file=session_file, path=path, log=log)
datasets[0] = dataset
# Check if the dataset has a categorical objective field and it
# has a max_categories limit for categories
if args.max_categories > 0 and len(datasets) == 1:
if pd.check_max_categories(fields.fields[args.objective_id_]):
distribution = pd.get_categories_distribution(dataset,
args.objective_id_)
if distribution and len(distribution) > args.max_categories:
categories = [element[0] for element in distribution]
other_label = pd.create_other_label(categories, other_label)
datasets, resume = pd.create_categories_datasets(
dataset, distribution, fields, args,
api, resume, session_file=session_file, path=path, log=log,
other_label=other_label)
else:
sys.exit("The provided objective field is not categorical nor "
"a full terms only text field. "
"Only these fields can be used with"
" --max-categories")
# If any of the transformations is applied,
# generate a new dataset from the given list of datasets
if args.new_dataset:
dataset, resume = pd.create_new_dataset(
datasets, api, args, resume, fields=fields,
session_file=session_file, path=path, log=log)
datasets = [dataset]
# Check if the dataset has a generators file associated with it, and
# generate a new dataset with the specified field structure. Also
# if the --to-dataset flag is used to clone or sample the original dataset
if args.new_fields or args.sample_rate != 1 or \
(args.lisp_filter or args.json_filter) and not has_source(args):
if fields is None:
if isinstance(dataset, basestring):
dataset = u.check_resource(dataset, api=api)
fields = Fields(dataset, csv_properties)
args.objective_id_ = get_objective_id(args, fields)
args.objective_name_ = fields.field_name(args.objective_id_)
dataset, resume = pd.create_new_dataset(
dataset, api, args, resume, fields=fields,
session_file=session_file, path=path, log=log)
datasets[0] = dataset
# rebuild fields structure for new ids and fields
csv_properties.update({'objective_field': args.objective_name_,
'objective_field_present': True})
fields = pd.get_fields_structure(dataset, csv_properties)
args.objective_id_ = get_objective_id(args, fields)
if args.multi_label and dataset and multi_label_data is None:
multi_label_data = l.get_multi_label_data(dataset)
(args.objective_field,
labels,
all_labels,
multi_label_fields) = l.multi_label_sync(args.objective_field,
labels,
multi_label_data,
fields, multi_label_fields)
if dataset:
# retrieves max_categories data, if any
args.max_categories = get_metadata(dataset, 'max_categories',
args.max_categories)
other_label = get_metadata(dataset, 'other_label',
other_label)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
logistic_regression = None
logistic_regressions = None
# no multi-label support at present
# variables from command-line options
resume = args.resume_
logistic_regression_ids = args.logistic_regression_ids_
output = args.predictions
# there's only one logistic regression to be generated at present
args.max_parallel_logistic_regressions = 1
# logistic regressions cannot be published yet.
args.public_logistic_regression = False
# It is compulsory to have a description to publish either datasets or
# logistic regressions
if (not args.description_
and (args.public_logistic_regression or args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
if args.objective_field:
csv_properties.update({'objective_field': args.objective_field})
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(api, args, resume, source,
csv_properties, fields,
session_file, path, log)
(_, datasets, test_dataset, resume, csv_properties,
fields) = dataset_properties
if datasets:
# Now we have a dataset, let's check if there's an objective_field
# given by the user and update it in the fields structure
args.objective_id_ = get_objective_id(args, fields)
if args.logistic_file:
# logistic regression is retrieved from the contents of the given local
# JSON file
logistic_regression, csv_properties, fields = u.read_local_resource(
args.logistic_file, csv_properties=csv_properties)
logistic_regressions = [logistic_regression]
logistic_regression_ids = [logistic_regression['resource']]
else:
# logistic regression is retrieved from the remote object
logistic_regressions, logistic_regression_ids, resume = \
plr.logistic_regressions_processing( \
datasets, logistic_regressions, logistic_regression_ids, \
api, args, resume, fields=fields, \
session_file=session_file, path=path, log=log)
if logistic_regressions:
logistic_regression = logistic_regressions[0]
# We update the logistic regression's public state if needed
if logistic_regression:
if isinstance(logistic_regression, basestring):
if not a.has_test(args):
query_string = MINIMUM_MODEL
elif args.export_fields:
query_string = r.ALL_FIELDS_QS
else:
query_string = ''
logistic_regression = u.check_resource(logistic_regression,
api.get_logistic_regression,
query_string=query_string)
logistic_regressions[0] = logistic_regression
if (args.public_logistic_regression
or (args.shared_flag
and r.shared_changed(args.shared, logistic_regression))):
logistic_regression_args = {}
if args.shared_flag and r.shared_changed(args.shared,
logistic_regression):
logistic_regression_args.update(shared=args.shared)
if args.public_logistic_regression:
logistic_regression_args.update( \
r.set_publish_logistic_regression_args(args))
if logistic_regression_args:
logistic_regression = r.update_logistic_regression( \
logistic_regression, logistic_regression_args, args,
api=api, path=path, \
session_file=session_file)
logistic_regressions[0] = logistic_regression
# We get the fields of the logistic_regression if we haven't got
# them yet and need them
if logistic_regression and (args.test_set or args.export_fields):
fields = plr.get_logistic_fields( \
logistic_regression, csv_properties, args)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
# If predicting
if logistic_regressions and (a.has_test(args) or \
(test_dataset and args.remote)):
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote predictions: predictions are computed as batch predictions
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api,
args,
resume,
name=test_name,
session_file=session_file,
path=path,
log=log)
(test_source, resume, csv_properties,
test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source,
"test",
dataset_args,
api,
args,
resume,
session_file=session_file,
path=path,
log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
csv_properties.update(objective_field=None,
objective_field_present=False)
test_fields = pd.get_fields_structure(test_dataset, csv_properties)
batch_prediction_args = r.set_batch_prediction_args(
args, fields=fields, dataset_fields=test_fields)
remote_lr_prediction(logistic_regression, test_dataset, \
batch_prediction_args, args, \
api, resume, prediction_file=output, \
session_file=session_file, path=path, log=log)
else:
lr_prediction(logistic_regressions,
fields,
args,
session_file=session_file)
# If evaluate flag is on, create remote evaluation and save results in
# json and human-readable format.
if args.evaluate:
# When we resume evaluation and models were already completed, we
# should use the datasets array as test datasets
if args.has_test_datasets_:
test_dataset = get_test_dataset(args)
if args.dataset_off and not args.has_test_datasets_:
args.test_dataset_ids = datasets
if args.test_dataset_ids and args.dataset_off:
# Evaluate the models with the corresponding test datasets.
test_dataset_id = bigml.api.get_dataset_id( \
args.test_dataset_ids[0])
test_dataset = api.check_resource(test_dataset_id)
csv_properties.update(objective_field=None,
objective_field_present=False)
test_fields = pd.get_fields_structure(test_dataset, csv_properties)
resume = evaluate(logistic_regressions,
args.test_dataset_ids,
api,
args,
resume,
fields=fields,
dataset_fields=test_fields,
session_file=session_file,
path=path,
log=log,
objective_field=args.objective_field)
else:
dataset = datasets[0]
if args.test_split > 0 or args.has_test_datasets_:
dataset = test_dataset
dataset = u.check_resource(dataset,
api=api,
query_string=r.ALL_FIELDS_QS)
dataset_fields = pd.get_fields_structure(dataset, None)
resume = evaluate(logistic_regressions, [dataset],
api,
args,
resume,
fields=fields,
dataset_fields=dataset_fields,
session_file=session_file,
path=path,
log=log,
objective_field=args.objective_field)
u.print_generated_files(path,
log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
cluster = None
clusters = None
# no multi-label support at present
# variables from command-line options
resume = args.resume_
cluster_ids = args.cluster_ids_
output = args.predictions
# there's only one cluster to be generated at present
args.max_parallel_clusters = 1
# clusters cannot be published yet.
args.public_cluster = False
# It is compulsory to have a description to publish either datasets or
# clusters
if (not args.description_
and (args.public_cluster or args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(api, args, resume, source,
csv_properties, fields,
session_file, path, log)
(_, datasets, test_dataset, resume, csv_properties,
fields) = dataset_properties
if args.cluster_file:
# cluster is retrieved from the contents of the given local JSON file
cluster, csv_properties, fields = u.read_local_resource(
args.cluster_file, csv_properties=csv_properties)
clusters = [cluster]
cluster_ids = [cluster['resource']]
else:
# cluster is retrieved from the remote object
clusters, cluster_ids, resume = pc.clusters_processing(
datasets,
clusters,
cluster_ids,
api,
args,
resume,
fields=fields,
session_file=session_file,
path=path,
log=log)
if clusters:
cluster = clusters[0]
# We update the cluster's public state if needed
if cluster:
if isinstance(cluster, basestring):
if args.cluster_datasets is None and not a.has_test(args):
query_string = MINIMUM_MODEL
else:
query_string = ''
cluster = u.check_resource(cluster,
api.get_cluster,
query_string=query_string)
clusters[0] = cluster
if (args.public_cluster or
(args.shared_flag and r.shared_changed(args.shared, cluster))):
cluster_args = {}
if args.shared_flag and r.shared_changed(args.shared, cluster):
cluster_args.update(shared=args.shared)
if args.public_cluster:
cluster_args.update(r.set_publish_cluster_args(args))
if cluster_args:
cluster = r.update_cluster(cluster,
cluster_args,
args,
api=api,
path=path,
session_file=session_file)
clusters[0] = cluster
# We get the fields of the cluster if we haven't got
# them yet and need them
if cluster and (args.test_set or args.export_fields):
if isinstance(cluster, dict):
cluster = cluster['resource']
cluster = u.check_resource(cluster,
api.get_cluster,
query_string=r.ALL_FIELDS_QS)
fields = pc.get_cluster_fields(cluster, csv_properties, args)
# If predicting
if clusters and (a.has_test(args) or (test_dataset and args.remote)):
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote centroids: centroids are computed as batch centroids
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api,
args,
resume,
name=test_name,
session_file=session_file,
path=path,
log=log)
(test_source, resume, csv_properties,
test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source,
"test",
dataset_args,
api,
args,
resume,
session_file=session_file,
path=path,
log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
test_fields = pd.get_fields_structure(test_dataset, csv_properties)
batch_centroid_args = r.set_batch_centroid_args(
args, fields=fields, dataset_fields=test_fields)
remote_centroid(cluster,
test_dataset,
batch_centroid_args,
args,
api,
resume,
prediction_file=output,
session_file=session_file,
path=path,
log=log)
else:
centroid(clusters, fields, args, session_file=session_file)
if cluster and args.cluster_datasets is not None:
cluster = api.check_resource(cluster)
centroids_info = cluster['object']['clusters']['clusters']
centroids = {
centroid['name']: centroid['id']
for centroid in centroids_info
}
cluster_datasets = cluster['object']['cluster_datasets']
if args.cluster_datasets == '':
centroid_ids = centroids.values()
else:
centroid_ids = [
centroids[cluster_name]
for cluster_name in args.cluster_datasets_
if cluster_datasets.get(centroids[cluster_name], '') == ''
]
for centroid_id in centroid_ids:
dataset_args = {'centroid': centroid_id}
r.create_dataset(cluster,
dataset_args,
args,
api=api,
path=path,
session_file=session_file,
log=log,
dataset_type='cluster')
if cluster and args.cluster_models is not None:
cluster = api.check_resource(cluster)
centroids_info = cluster['object']['clusters']['clusters']
centroids = {
centroid['name']: centroid['id']
for centroid in centroids_info
}
models = cluster['object']['cluster_models']
if args.cluster_models == '':
centroid_ids = centroids.values()
else:
centroid_ids = [
centroids[cluster_name]
for cluster_name in args.cluster_models_
if models.get(centroids[cluster_name], '') == ''
]
for centroid_id in centroid_ids:
model_args = {'centroid': centroid_id}
r.create_model(cluster,
model_args,
args,
api=api,
path=path,
session_file=session_file,
log=log,
model_type='cluster')
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
u.print_generated_files(path,
log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates a sample based on a `train_set`, source or dataset.
"""
samples = None
# variables from command-line options
resume = args.resume_
sample_ids = args.sample_ids_
output = args.predictions
# there's only one sample to be generated at present
args.max_parallel_clusters = 1
# sample cannot be published yet.
args.public_sample = False
# It is compulsory to have a description to publish either datasets or
# clusters
if (not args.description_ and (args.public_sample or args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-sample step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-sample step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(api, args, resume, source,
csv_properties, fields,
session_file, path, log)
(_, datasets, _, resume, csv_properties, fields) = dataset_properties
if args.sample_file:
# sample is retrieved from the contents of the given local JSON file
sample, csv_properties, fields = u.read_local_resource(
args.sample_file, csv_properties=csv_properties)
samples = [sample]
sample_ids = [sample['resource']]
else:
# sample is retrieved from the remote object
samples, sample_ids, resume = psa.samples_processing(
datasets,
samples,
sample_ids,
api,
args,
resume,
session_file=session_file,
path=path,
log=log)
if samples:
sample = samples[0]
# We update the sample's public state if needed
if sample:
if isinstance(sample, basestring):
# build the query string from the sample options
sample = u.check_resource(sample, api.get_sample)
samples[0] = sample
if (args.public_sample or
(args.shared_flag and r.shared_changed(args.shared, sample))):
sample_args = {}
if args.shared_flag and r.shared_changed(args.shared, sample):
sample_args.update(shared=args.shared)
if args.public_sample:
sample_args.update(r.set_publish_sample_args(args))
if sample_args:
sample = r.update_sample(sample,
sample_args,
args,
api=api,
path=path,
session_file=session_file)
samples[0] = sample
# We get the fields of the sample if we haven't got
# them yet and need them
if sample and psa.needs_sample_fields(args):
fields = psa.get_sample_fields(sample, csv_properties, args)
sample_file(samples[0],
fields,
args,
api,
path=path,
session_file=session_file)
u.print_generated_files(path,
log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
association = None
associations = None
# no multi-label support at present
# variables from command-line options
resume = args.resume_
association_ids = args.association_ids_
output = args.predictions
# there's only one association resource to be generated at present
args.max_parallel_associations = 1
# associations cannot be published yet.
args.public_association = False
# It is compulsory to have a description to publish either datasets or
# associations
if (not args.description_ and (args.public_association or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(_, datasets, test_dataset,
resume, csv_properties, fields) = dataset_properties
if args.association_file:
# association is retrieved from the contents of the given local JSON
# file
association, csv_properties, fields = u.read_local_resource(
args.association_file,
csv_properties=csv_properties)
associations = [association]
association_ids = [association['resource']]
else:
# association is retrieved from the remote object
associations, association_ids, resume = pa.associations_processing(
datasets, associations, association_ids, api, args, resume,
fields=fields,
session_file=session_file, path=path, log=log)
if associations:
association = associations[0]
# We update the association's public state if needed
if association:
if isinstance(association, basestring):
if not a.has_test(args):
query_string = MINIMUM_MODEL
else:
query_string = ''
association = u.check_resource(association, api.get_association,
query_string=query_string)
associations[0] = association
if (args.public_association or
(args.shared_flag and
r.shared_changed(args.shared, association))):
association_args = {}
if args.shared_flag and \
r.shared_changed(args.shared, association):
association_args.update(shared=args.shared)
if args.public_association:
association_args.update(ras.set_publish_association_args(args))
if association_args:
association = ras.update_association( \
association, association_args, args,
api=api, path=path,
session_file=session_file)
associations[0] = association
# We get the fields of the association if we haven't got
# them yet and need them
if association and args.test_set:
fields = pa.get_association_fields(association, csv_properties, args)
# If predicting
if associations and (a.has_test(args) or (test_dataset and args.remote)):
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote association sets: association sets are computed as
# batch association sets
# in bigml.com except when --no-batch flag is set. They are currently
# not supported yet
if args.remote and not args.no_batch:
sys.exit("Batch association sets are currently not supported.")
else:
sys.exit("Local prediction of association sets is currently"
" not supported.")
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
time_series = None
time_series_set = None
# variables from command-line options
resume = args.resume_
time_series_ids = args.time_series_ids_
output = args.predictions
# there's only one time_series to be generated at present
args.max_parallel_time_series = 1
args.max_parallel_evaluations = 1
# time_series cannot be published yet.
args.public_time_series = False
# no cross-validations
args.dataset_off = False
args.cross_validation_rate = 0
args.number_of_evaluations = 1
# It is compulsory to have a description to publish either datasets or
# time_series
if (not args.description_ and (args.public_time_series or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
if args.objective_field:
csv_properties.update({'objective_field': args.objective_field})
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(_, datasets, test_dataset,
resume, csv_properties, fields) = dataset_properties
if datasets:
# Now we have a dataset, let's check if there's an objective_field
# given by the user and update it in the fields structure
args.objective_id_ = get_objective_id(args, fields)
# if the time series is going to be evaluated, and we don't have
# test data, we need to divide the rows using ranges, so we'll need
# max rows
args.max_rows = datasets[0]["object"]["rows"]
if args.time_series_file:
# time-series is retrieved from the contents of the given local
# JSON file
time_series, csv_properties, fields = u.read_local_resource(
args.time_series_file,
csv_properties=csv_properties)
time_series_set = [time_series]
time_series_ids = [time_series['resource']]
else:
# time-series is retrieved from the remote object
time_series_set, time_series_ids, resume = \
pts.time_series_processing( \
datasets, time_series_set, time_series_ids, \
api, args, resume, fields=fields, \
session_file=session_file, path=path, log=log)
if time_series_set:
time_series = time_series_set[0]
# We update the time-series' public state if needed
if time_series:
if isinstance(time_series, basestring):
query_string = r.ALL_FIELDS_QS
time_series = u.check_resource(time_series,
api.get_time_series,
query_string=query_string)
time_series_set[0] = time_series
if (args.public_time_series or
(args.shared_flag and r.shared_changed(args.shared,
time_series))):
time_series_args = {}
if args.shared_flag and r.shared_changed(args.shared,
time_series):
time_series_args.update(shared=args.shared)
if args.public_time_series:
time_series_args.update( \
r.set_publish_time_series_args(args))
if time_series_args:
time_series = r.time_series( \
time_series, time_series_args, args,
api=api, path=path, \
session_file=session_file)
time_series_set[0] = time_series
"""
# We get the fields of the time-series if we haven't got
# them yet and need them
if time_series and (args.test_set or args.export_fields):
fields = pts.get_time_series_fields( \
time_series, csv_properties, args)
"""
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
# If forecasting
if time_series_set and a.has_ts_test(args):
if args.remote:
forecast_args = r.set_forecast_args(
args, fields=fields)
remote_forecast(time_series, forecast_args, args, \
api, resume, prediction_file=output, \
session_file=session_file, path=path, log=log)
else:
forecast(time_series, args,
session_file=session_file)
# If evaluate flag is on, create remote evaluation and save results in
# json and human-readable format.
if args.evaluate:
# When we resume evaluation and models were already completed, we
# should use the datasets array as test datasets
if args.has_test_datasets_:
test_dataset = get_test_dataset(args)
if args.dataset_off and not args.has_test_datasets_:
args.test_dataset_ids = datasets
if args.test_dataset_ids and args.dataset_off:
# Evaluate the models with the corresponding test datasets.
test_dataset_id = bigml.api.get_dataset_id( \
args.test_dataset_ids[0])
test_dataset = api.check_resource(test_dataset_id)
csv_properties.update(objective_field=None,
objective_field_present=False)
test_fields = pd.get_fields_structure(test_dataset,
csv_properties)
resume = evaluate(time_series_set, args.test_dataset_ids, api,
args, resume,
fields=fields, dataset_fields=test_fields,
session_file=session_file, path=path,
log=log,
objective_field=args.objective_field)
else:
dataset = datasets[0]
if args.test_split > 0 or args.has_test_datasets_:
dataset = test_dataset
else:
args.range_ = [int(args.max_rows * r.EVALUATE_SAMPLE_RATE),
args.max_rows]
dataset = u.check_resource(dataset, api=api,
query_string=r.ALL_FIELDS_QS)
dataset_fields = pd.get_fields_structure(dataset, None)
resume = evaluate(time_series_set, [dataset], api,
args, resume,
fields=fields, dataset_fields=dataset_fields,
session_file=session_file, path=path,
log=log,
objective_field=args.objective_field)
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates a dataset using the `training_set`.
"""
source = None
dataset = None
fields = None
other_label = OTHER
multi_label_data = None
multi_label_fields = []
datasets = None
# variables from command-line options
resume = args.resume_
output = args.output
dataset_fields = args.dataset_fields_
check_args_coherence(args)
path = u.check_dir(output)
session_file = "%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# labels to be used in multi-label expansion
labels = (None if args.labels is None else [
label.strip() for label in args.labels.split(args.args_separator)
])
if labels is not None:
labels = sorted([label for label in labels])
# multi_label file must be preprocessed to obtain a new extended file
if args.multi_label and args.training_set is not None:
(args.training_set, multi_label_data) = ps.multi_label_expansion(
args.training_set,
args.train_header,
args,
path,
labels=labels,
session_file=session_file)
args.train_header = True
args.objective_field = multi_label_data["objective_name"]
all_labels = l.get_all_labels(multi_label_data)
if not labels:
labels = all_labels
else:
all_labels = labels
if args.objective_field:
csv_properties.update({'objective_field': args.objective_field})
if args.source_file:
# source is retrieved from the contents of the given local JSON file
source, csv_properties, fields = u.read_local_resource(
args.source_file, csv_properties=csv_properties)
else:
# source is retrieved from the remote object
source, resume, csv_properties, fields = ps.source_processing(
api,
args,
resume,
csv_properties=csv_properties,
multi_label_data=multi_label_data,
session_file=session_file,
path=path,
log=log)
if source is not None:
args.source = bigml.api.get_source_id(source)
if args.multi_label and source:
multi_label_data = l.get_multi_label_data(source)
(args.objective_field, labels, all_labels,
multi_label_fields) = l.multi_label_sync(args.objective_field, labels,
multi_label_data, fields,
multi_label_fields)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
if args.dataset_file:
# dataset is retrieved from the contents of the given local JSON file
model_dataset, csv_properties, fields = u.read_local_resource(
args.dataset_file, csv_properties=csv_properties)
if not args.datasets:
datasets = [model_dataset]
dataset = model_dataset
else:
datasets = u.read_datasets(args.datasets)
if not datasets:
# dataset is retrieved from the remote object
datasets, resume, csv_properties, fields = pd.dataset_processing(
source,
api,
args,
resume,
fields=fields,
csv_properties=csv_properties,
multi_label_data=multi_label_data,
session_file=session_file,
path=path,
log=log)
if datasets:
dataset = datasets[-1]
if args.to_csv is not None:
resume = pd.export_dataset(dataset,
api,
args,
resume,
session_file=session_file,
path=path)
# Now we have a dataset, let's check if there's an objective_field
# given by the user and update it in the fields structure
args.objective_id_ = get_objective_id(args, fields)
# If test_split is used, split the dataset in a training and a test dataset
# according to the given split
if args.test_split > 0:
dataset, test_dataset, resume = pd.split_processing(
dataset,
api,
args,
resume,
multi_label_data=multi_label_data,
session_file=session_file,
path=path,
log=log)
datasets[0] = dataset
# Check if the dataset has a categorical objective field and it
# has a max_categories limit for categories
if args.max_categories > 0 and len(datasets) == 1:
if pd.check_max_categories(fields.fields[args.objective_id_]):
distribution = pd.get_categories_distribution(
dataset, args.objective_id_)
if distribution and len(distribution) > args.max_categories:
categories = [element[0] for element in distribution]
other_label = pd.create_other_label(categories, other_label)
datasets, resume = pd.create_categories_datasets(
dataset,
distribution,
fields,
args,
api,
resume,
session_file=session_file,
path=path,
log=log,
other_label=other_label)
else:
sys.exit("The provided objective field is not categorical nor "
"a full terms only text field. "
"Only these fields can be used with"
" --max-categories")
# If any of the transformations is applied,
# generate a new dataset from the given list of datasets
if args.new_dataset:
dataset, resume = pd.create_new_dataset(datasets,
api,
args,
resume,
fields=fields,
session_file=session_file,
path=path,
log=log)
datasets = [dataset]
# Check if the dataset has a generators file associated with it, and
# generate a new dataset with the specified field structure. Also
# if the --to-dataset flag is used to clone or sample the original dataset
if args.new_fields or args.sample_rate != 1 or \
(args.lisp_filter or args.json_filter) and not has_source(args):
if fields is None:
if isinstance(dataset, basestring):
dataset = u.check_resource(dataset, api=api)
fields = Fields(dataset, csv_properties)
args.objective_id_ = get_objective_id(args, fields)
args.objective_name_ = fields.field_name(args.objective_id_)
dataset, resume = pd.create_new_dataset(dataset,
api,
args,
resume,
fields=fields,
session_file=session_file,
path=path,
log=log)
datasets[0] = dataset
# rebuild fields structure for new ids and fields
csv_properties.update({
'objective_field': args.objective_name_,
'objective_field_present': True
})
fields = pd.get_fields_structure(dataset, csv_properties)
args.objective_id_ = get_objective_id(args, fields)
if args.multi_label and dataset and multi_label_data is None:
multi_label_data = l.get_multi_label_data(dataset)
(args.objective_field, labels, all_labels,
multi_label_fields) = l.multi_label_sync(args.objective_field, labels,
multi_label_data, fields,
multi_label_fields)
if dataset:
# retrieves max_categories data, if any
args.max_categories = get_metadata(dataset, 'max_categories',
args.max_categories)
other_label = get_metadata(dataset, 'other_label', other_label)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
u.print_generated_files(path,
log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def reify_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different processing functions
"""
command = command_handling(args, COMMAND_LOG)
# Parses command line arguments.
command_args = a.parse_and_check(command)
if command_args.resume:
command_args, session_file, _ = get_stored_command(
args, command_args.debug, command_log=COMMAND_LOG,
dirs_log=DIRS_LOG, sessions_log=SESSIONS_LOG)
if command_args.output is None:
command_args.output = os.path.join(command_args.output_dir,
DEFAULT_OUTPUT)
else:
if command_args.output_dir is None:
command_args.output_dir = a.NOW
if command_args.output is None:
command_args.output = os.path.join(command_args.output_dir,
DEFAULT_OUTPUT)
if len(os.path.dirname(command_args.output).strip()) == 0:
command_args.output = os.path.join(command_args.output_dir,
command_args.output)
directory = u.check_dir(command_args.output)
command_args.output_dir = directory
session_file = os.path.join(directory, SESSIONS_LOG)
u.log_message(command.command + "\n", log_file=session_file)
directory = u.check_dir(os.path.join(command_args.output_dir, "tmp"))
session_file = os.path.join(directory, SESSIONS_LOG)
u.log_message(command.command + "\n", log_file=session_file)
try:
shutil.copy(DEFAULTS_FILE, os.path.join(directory, DEFAULTS_FILE))
except IOError:
pass
u.sys_log_message(u"%s\n" % os.path.abspath(directory),
log_file=DIRS_LOG)
# If --clear-logs the log files are cleared
if "--clear-logs" in args:
clear_log_files(LOG_FILES)
def logger(message):
"""Partial to log messages according to args.verbosity
"""
u.log_message(u.dated(message), \
log_file=session_file, console=command_args.verbosity)
# Creates the corresponding api instance
api = a.get_api_instance(command_args, u.check_dir(session_file))
message = "Starting reification for %s\n\n" % command_args.resource_id
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
reify_resources(command_args, api, logger)
message = "\nReification complete. See the results in %s\n\n" % \
command_args.output
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir, log_file=session_file,
verbosity=command_args.verbosity)
def compute_output(api, args):
""" Creates a fusion using the `models` list or uses the ids
of a previously created BigML fusion to make predictions for the `test_set`.
"""
fusion = None
# variables from command-line options
resume = args.resume_
fusion_ids = args.fusion_ids_
output = args.predictions
# there's only one fusion to be generated at present
args.max_parallel_fusions = 1
# fusion cannot be published yet.
args.public_fusion = False
# It is compulsory to have a description to publish either datasets or
# fusions
if (not args.description_ and args.public_fusion):
sys.exit("You should provide a description to publish.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
if args.fusion_file:
# fusion regression is retrieved from the contents of the given local
# JSON file
fusion, csv_properties, fields = u.read_local_resource(
args.fusion_file,
csv_properties=csv_properties)
fusion_ids = [fusion]
else:
# fusion is retrieved from the remote object or created
fusion, resume = \
pf.fusion_processing( \
fusion, fusion_ids, \
api, args, resume, \
session_file=session_file, path=path, log=log)
# We update the fusion public state if needed
if fusion:
if isinstance(fusion, basestring):
if not a.has_test(args):
query_string = MINIMUM_MODEL
elif args.export_fields:
query_string = r.ALL_FIELDS_QS
else:
query_string = ''
fusion = u.check_resource(fusion,
api.get_fusion,
query_string=query_string)
if (args.public_fusion or
(args.shared_flag and r.shared_changed(args.shared,
fusion))):
fusion_args = {}
if args.shared_flag and r.shared_changed(args.shared,
fusion):
fusion_args.update(shared=args.shared)
if args.public_fusion:
fusion_args.update( \
r.set_publish_fusion_args(args))
if fusion_args:
fusion = r.update_fusion( \
fusion, fusion_args, args,
api=api, path=path, \
session_file=session_file)
# We get the fields of the fusion if we haven't got
# them yet and need them
if fusion and (args.test_set or args.evaluate):
fields = pf.get_fusion_fields( \
fusion, csv_properties, args)
# If predicting
if fusion and (a.has_test(args) or \
args.remote):
test_dataset = get_test_dataset(args)
# Remote predictions: predictions are computed as batch predictions
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api, args, resume, name=test_name,
session_file=session_file, path=path, log=log)
(test_source, resume,
csv_properties, test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source, "test", dataset_args, api, args,
resume, session_file=session_file, path=path, log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
csv_properties.update(objective_field=None,
objective_field_present=False)
test_fields = pd.get_fields_structure(test_dataset,
csv_properties)
if not args.evaluate:
batch_prediction_args = r.set_batch_prediction_args(
args, fields=fields,
dataset_fields=test_fields)
remote_prediction(fusion, test_dataset, \
batch_prediction_args, args, \
api, resume, prediction_file=output, \
session_file=session_file, path=path, log=log)
else:
prediction([fusion], fields, args,
session_file=session_file)
# If evaluate flag is on, create remote evaluation and save results in
# json and human-readable format.
if args.evaluate:
# When we resume evaluation and models were already completed, we
# should use the datasets array as test datasets
args.max_parallel_evaluations = 1 # only one evaluation at present
args.cross_validation_rate = 0 # no cross-validation
args.number_of_evaluations = 1 # only one evaluation
if args.has_test_datasets_:
test_dataset = get_test_dataset(args)
dataset = test_dataset
dataset = u.check_resource(dataset, api=api,
query_string=r.ALL_FIELDS_QS)
dataset_fields = pd.get_fields_structure(dataset, None)
resume = evaluate([fusion], [dataset], api,
args, resume,
fields=fields, dataset_fields=dataset_fields,
session_file=session_file, path=path,
log=log,
objective_field=args.objective_field)
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates a fusion using the `models` list or uses the ids
of a previously created BigML fusion to make predictions for the `test_set`.
"""
fusion = None
# variables from command-line options
resume = args.resume_
fusion_ids = args.fusion_ids_
output = args.predictions
# there's only one fusion to be generated at present
args.max_parallel_fusions = 1
# fusion cannot be published yet.
args.public_fusion = False
# It is compulsory to have a description to publish either datasets or
# fusions
if (not args.description_ and args.public_fusion):
sys.exit("You should provide a description to publish.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
if args.fusion_file:
# fusion regression is retrieved from the contents of the given local
# JSON file
fusion, csv_properties, fields = u.read_local_resource(
args.fusion_file, csv_properties=csv_properties)
fusion_ids = [fusion]
else:
# fusion is retrieved from the remote object or created
fusion, resume = \
pf.fusion_processing( \
fusion, fusion_ids, \
api, args, resume, \
session_file=session_file, path=path, log=log)
# We update the fusion public state if needed
if fusion:
if isinstance(fusion, basestring):
if not a.has_test(args):
query_string = MINIMUM_MODEL
elif args.export_fields:
query_string = r.ALL_FIELDS_QS
else:
query_string = ''
fusion = u.check_resource(fusion,
api.get_fusion,
query_string=query_string)
if (args.public_fusion or
(args.shared_flag and r.shared_changed(args.shared, fusion))):
fusion_args = {}
if args.shared_flag and r.shared_changed(args.shared, fusion):
fusion_args.update(shared=args.shared)
if args.public_fusion:
fusion_args.update( \
r.set_publish_fusion_args(args))
if fusion_args:
fusion = r.update_fusion( \
fusion, fusion_args, args,
api=api, path=path, \
session_file=session_file)
# We get the fields of the fusion if we haven't got
# them yet and need them
if fusion and (args.test_set or args.evaluate):
fields = pf.get_fusion_fields( \
fusion, csv_properties, args)
# If predicting
if fusion and (a.has_test(args) or \
args.remote):
test_dataset = get_test_dataset(args)
# Remote predictions: predictions are computed as batch predictions
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api,
args,
resume,
name=test_name,
session_file=session_file,
path=path,
log=log)
(test_source, resume, csv_properties,
test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source,
"test",
dataset_args,
api,
args,
resume,
session_file=session_file,
path=path,
log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
csv_properties.update(objective_field=None,
objective_field_present=False)
test_fields = pd.get_fields_structure(test_dataset, csv_properties)
if not args.evaluate:
batch_prediction_args = r.set_batch_prediction_args(
args, fields=fields, dataset_fields=test_fields)
remote_prediction(fusion, test_dataset, \
batch_prediction_args, args, \
api, resume, prediction_file=output, \
session_file=session_file, path=path, log=log)
else:
prediction([fusion], fields, args, session_file=session_file)
# If evaluate flag is on, create remote evaluation and save results in
# json and human-readable format.
if args.evaluate:
# When we resume evaluation and models were already completed, we
# should use the datasets array as test datasets
args.max_parallel_evaluations = 1 # only one evaluation at present
args.cross_validation_rate = 0 # no cross-validation
args.number_of_evaluations = 1 # only one evaluation
if args.has_test_datasets_:
test_dataset = get_test_dataset(args)
dataset = test_dataset
dataset = u.check_resource(dataset,
api=api,
query_string=r.ALL_FIELDS_QS)
dataset_fields = pd.get_fields_structure(dataset, None)
resume = evaluate([fusion], [dataset],
api,
args,
resume,
fields=fields,
dataset_fields=dataset_fields,
session_file=session_file,
path=path,
log=log,
objective_field=args.objective_field)
u.print_generated_files(path,
log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
logistic_regression = None
logistic_regressions = None
# no multi-label support at present
# variables from command-line options
resume = args.resume_
logistic_regression_ids = args.logistic_regression_ids_
output = args.predictions
# there's only one logistic regression to be generated at present
args.max_parallel_logistic_regressions = 1
# logistic regressions cannot be published yet.
args.public_logistic_regression = False
# It is compulsory to have a description to publish either datasets or
# logistic regressions
if (not args.description_ and (args.public_logistic_regression or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
if args.objective_field:
csv_properties.update({'objective_field': args.objective_field})
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(_, datasets, test_dataset,
resume, csv_properties, fields) = dataset_properties
if datasets:
# Now we have a dataset, let's check if there's an objective_field
# given by the user and update it in the fields structure
args.objective_id_ = get_objective_id(args, fields)
if args.logistic_file:
# logistic regression is retrieved from the contents of the given local
# JSON file
logistic_regression, csv_properties, fields = u.read_local_resource(
args.logistic_file,
csv_properties=csv_properties)
logistic_regressions = [logistic_regression]
logistic_regression_ids = [logistic_regression['resource']]
else:
# logistic regression is retrieved from the remote object
logistic_regressions, logistic_regression_ids, resume = \
plr.logistic_regressions_processing( \
datasets, logistic_regressions, logistic_regression_ids, \
api, args, resume, fields=fields, \
session_file=session_file, path=path, log=log)
if logistic_regressions:
logistic_regression = logistic_regressions[0]
# We update the logistic regression's public state if needed
if logistic_regression:
if isinstance(logistic_regression, basestring):
if not a.has_test(args):
query_string = MINIMUM_MODEL
elif args.export_fields:
query_string = r.ALL_FIELDS_QS
else:
query_string = ''
logistic_regression = u.check_resource(logistic_regression,
api.get_logistic_regression,
query_string=query_string)
logistic_regressions[0] = logistic_regression
if (args.public_logistic_regression or
(args.shared_flag and r.shared_changed(args.shared,
logistic_regression))):
logistic_regression_args = {}
if args.shared_flag and r.shared_changed(args.shared,
logistic_regression):
logistic_regression_args.update(shared=args.shared)
if args.public_logistic_regression:
logistic_regression_args.update( \
r.set_publish_logistic_regression_args(args))
if logistic_regression_args:
logistic_regression = r.update_logistic_regression( \
logistic_regression, logistic_regression_args, args,
api=api, path=path, \
session_file=session_file)
logistic_regressions[0] = logistic_regression
# We get the fields of the logistic_regression if we haven't got
# them yet and need them
if logistic_regression and (args.test_set or args.export_fields):
fields = plr.get_logistic_fields( \
logistic_regression, csv_properties, args)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
# If predicting
if logistic_regressions and (a.has_test(args) or \
(test_dataset and args.remote)):
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote predictions: predictions are computed as batch predictions
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api, args, resume, name=test_name,
session_file=session_file, path=path, log=log)
(test_source, resume,
csv_properties, test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source, "test", dataset_args, api, args,
resume, session_file=session_file, path=path, log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
csv_properties.update(objective_field=None,
objective_field_present=False)
test_fields = pd.get_fields_structure(test_dataset,
csv_properties)
batch_prediction_args = r.set_batch_prediction_args(
args, fields=fields,
dataset_fields=test_fields)
remote_lr_prediction(logistic_regression, test_dataset, \
batch_prediction_args, args, \
api, resume, prediction_file=output, \
session_file=session_file, path=path, log=log)
else:
lr_prediction(logistic_regressions, fields, args,
session_file=session_file)
# If evaluate flag is on, create remote evaluation and save results in
# json and human-readable format.
if args.evaluate:
# When we resume evaluation and models were already completed, we
# should use the datasets array as test datasets
if args.has_test_datasets_:
test_dataset = get_test_dataset(args)
if args.dataset_off and not args.has_test_datasets_:
args.test_dataset_ids = datasets
if args.test_dataset_ids and args.dataset_off:
# Evaluate the models with the corresponding test datasets.
resume = evaluate(logistic_regressions, args.test_dataset_ids, api,
args, resume,
fields=fields, dataset_fields=dataset_fields,
session_file=session_file, path=path,
log=log, labels=labels, all_labels=all_labels,
objective_field=args.objective_field)
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
pca = None
# variables from command-line options
resume = args.resume_
pca_ids = args.pca_ids_
output = args.projections
# there's only one pca to be generated at present
args.max_parallel_pcas = 1
# pca cannot be published yet.
args.public_pca = False
# It is compulsory to have a description to publish either datasets or
# pcas
if (not args.description_ and (args.public_pca or args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
if args.objective_field:
csv_properties.update({'objective_field': args.objective_field})
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(api, args, resume, source,
csv_properties, fields,
session_file, path, log)
(_, datasets, test_dataset, resume, csv_properties,
fields) = dataset_properties
if args.pca_file:
# pca regression is retrieved from the contents of the given local
# JSON file
pca, csv_properties, fields = u.read_local_resource(
args.pca_file, csv_properties=csv_properties)
pac_ids = [pca]
else:
# pca is retrieved from the remote object or created
pca, resume = \
pc.pca_processing( \
datasets, pca, pca_ids, \
api, args, resume, fields=fields, \
session_file=session_file, path=path, log=log)
# We update the pca public state if needed
if pca:
if isinstance(pca, basestring):
if not a.has_test(args):
query_string = MINIMUM_MODEL
elif args.export_fields:
query_string = r.ALL_FIELDS_QS
else:
query_string = ''
pca = u.check_resource(pca, api.get_pca, query_string=query_string)
if (args.public_pca
or (args.shared_flag and r.shared_changed(args.shared, pca))):
pca_args = {}
if args.shared_flag and r.shared_changed(args.shared, pca):
pca_args.update(shared=args.shared)
if args.public_pca:
pca_args.update( \
r.set_publish_pca_args(args))
if pca_args:
pca = r.update_pca( \
pca, pca_args, args,
api=api, path=path, \
session_file=session_file)
# We get the fields of the pca if we haven't got
# them yet and need them
if pca and (args.test_set or args.export_fields):
fields = pc.get_pca_fields( \
pca, csv_properties, args)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
# If predicting
if pca and (a.has_test(args) or \
(test_dataset and args.remote)):
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote projections: projections are computed as batch projections
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api,
args,
resume,
name=test_name,
session_file=session_file,
path=path,
log=log)
(test_source, resume, csv_properties,
test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source,
"test",
dataset_args,
api,
args,
resume,
session_file=session_file,
path=path,
log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
csv_properties.update(objective_field=None,
objective_field_present=False)
test_fields = pd.get_fields_structure(test_dataset, csv_properties)
batch_projection_args = r.set_batch_projection_args(
args, fields=fields, dataset_fields=test_fields)
remote_projection(pca, test_dataset, \
batch_projection_args, args, \
api, resume, projection_file=output, \
session_file=session_file, path=path, log=log)
else:
projection(pca, fields, args, session_file=session_file)
u.print_generated_files(path,
log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
time_series = None
time_series_set = None
# variables from command-line options
resume = args.resume_
time_series_ids = args.time_series_ids_
output = args.predictions
# there's only one time_series to be generated at present
args.max_parallel_time_series = 1
args.max_parallel_evaluations = 1
# time_series cannot be published yet.
args.public_time_series = False
# no cross-validations
args.dataset_off = False
args.cross_validation_rate = 0
args.number_of_evaluations = 1
# It is compulsory to have a description to publish either datasets or
# time_series
if (not args.description_
and (args.public_time_series or args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
if args.objective_field:
csv_properties.update({'objective_field': args.objective_field})
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(api, args, resume, source,
csv_properties, fields,
session_file, path, log)
(_, datasets, test_dataset, resume, csv_properties,
fields) = dataset_properties
if datasets:
# Now we have a dataset, let's check if there's an objective_field
# given by the user and update it in the fields structure
args.objective_id_ = get_objective_id(args, fields)
# if the time series is going to be evaluated, and we don't have
# test data, we need to divide the rows using ranges, so we'll need
# max rows
args.max_rows = datasets[0]["object"]["rows"]
if args.time_series_file:
# time-series is retrieved from the contents of the given local
# JSON file
time_series, csv_properties, fields = u.read_local_resource(
args.time_series_file, csv_properties=csv_properties)
time_series_set = [time_series]
time_series_ids = [time_series['resource']]
else:
# time-series is retrieved from the remote object
time_series_set, time_series_ids, resume = \
pts.time_series_processing( \
datasets, time_series_set, time_series_ids, \
api, args, resume, fields=fields, \
session_file=session_file, path=path, log=log)
if time_series_set:
time_series = time_series_set[0]
# We update the time-series' public state if needed
if time_series:
if isinstance(time_series, basestring):
query_string = r.ALL_FIELDS_QS
time_series = u.check_resource(time_series,
api.get_time_series,
query_string=query_string)
time_series_set[0] = time_series
if (args.public_time_series or
(args.shared_flag and r.shared_changed(args.shared, time_series))):
time_series_args = {}
if args.shared_flag and r.shared_changed(args.shared, time_series):
time_series_args.update(shared=args.shared)
if args.public_time_series:
time_series_args.update( \
r.set_publish_time_series_args(args))
if time_series_args:
time_series = r.time_series( \
time_series, time_series_args, args,
api=api, path=path, \
session_file=session_file)
time_series_set[0] = time_series
"""
# We get the fields of the time-series if we haven't got
# them yet and need them
if time_series and (args.test_set or args.export_fields):
fields = pts.get_time_series_fields( \
time_series, csv_properties, args)
"""
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
# If forecasting
if time_series_set and a.has_ts_test(args):
if args.remote:
forecast_args = r.set_forecast_args(args, fields=fields)
remote_forecast(time_series, forecast_args, args, \
api, resume, prediction_file=output, \
session_file=session_file, path=path, log=log)
else:
forecast(time_series, args, session_file=session_file)
# If evaluate flag is on, create remote evaluation and save results in
# json and human-readable format.
if args.evaluate:
# When we resume evaluation and models were already completed, we
# should use the datasets array as test datasets
if args.has_test_datasets_:
test_dataset = get_test_dataset(args)
if args.dataset_off and not args.has_test_datasets_:
args.test_dataset_ids = datasets
if args.test_dataset_ids and args.dataset_off:
# Evaluate the models with the corresponding test datasets.
test_dataset_id = bigml.api.get_dataset_id( \
args.test_dataset_ids[0])
test_dataset = api.check_resource(test_dataset_id)
csv_properties.update(objective_field=None,
objective_field_present=False)
test_fields = pd.get_fields_structure(test_dataset, csv_properties)
resume = evaluate(time_series_set,
args.test_dataset_ids,
api,
args,
resume,
fields=fields,
dataset_fields=test_fields,
session_file=session_file,
path=path,
log=log,
objective_field=args.objective_field)
else:
dataset = datasets[0]
if args.test_split > 0 or args.has_test_datasets_:
dataset = test_dataset
else:
args.range_ = [
int(args.max_rows * r.EVALUATE_SAMPLE_RATE), args.max_rows
]
dataset = u.check_resource(dataset,
api=api,
query_string=r.ALL_FIELDS_QS)
dataset_fields = pd.get_fields_structure(dataset, None)
resume = evaluate(time_series_set, [dataset],
api,
args,
resume,
fields=fields,
dataset_fields=dataset_fields,
session_file=session_file,
path=path,
log=log,
objective_field=args.objective_field)
u.print_generated_files(path,
log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
if args.test_split > 0 or args.has_test_datasets_:
dataset = test_dataset
dataset = u.check_resource(dataset, api=api,
query_string=r.ALL_FIELDS_QS)
dataset_fields = pd.get_fields_structure(dataset, None)
models_or_ensembles = (ensemble_ids if ensemble_ids != []
else models)
resume = evaluate(models_or_ensembles, [dataset], api,
args, resume,
fields=fields, dataset_fields=dataset_fields,
session_file=session_file, path=path,
log=log, labels=labels, all_labels=all_labels,
objective_field=args.objective_field)
# If cross_validation_rate is > 0, create remote evaluations and save
# results in json and human-readable format. Then average the results to
# issue a cross_validation measure set.
if args.cross_validation_rate > 0:
args.sample_rate = 1 - args.cross_validation_rate
cross_validate(models, dataset, fields, api, args, resume,
session_file=session_file,
path=path, log=log)
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def project_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different processing functions
"""
command = command_handling(args, COMMAND_LOG)
# Parses command line arguments.
command_args = a.parse_and_check(command)
if command_args.resume:
command_args, session_file, _ = get_stored_command(
args, command_args.debug, command_log=COMMAND_LOG,
dirs_log=DIRS_LOG, sessions_log=SESSIONS_LOG)
else:
if command_args.output_dir is None:
command_args.output_dir = a.NOW
directory = u.check_dir("%s/x.txt" % command_args.output_dir)
command_args.output_dir = directory
session_file = os.path.join(directory, SESSIONS_LOG)
u.log_message(command.command + "\n", log_file=session_file)
directory = u.check_dir(os.path.join(command_args.output_dir, "tmp"))
session_file = os.path.join(directory, SESSIONS_LOG)
u.log_message(command.command + "\n", log_file=session_file)
try:
shutil.copy(DEFAULTS_FILE, os.path.join(directory, DEFAULTS_FILE))
except IOError:
pass
u.sys_log_message(u"%s\n" % os.path.abspath(directory),
log_file=DIRS_LOG)
path = u.check_dir("%s/x.txt" % command_args.output_dir)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
# If logging is required set the file for logging
log = None
if command_args.log_file:
u.check_dir(command_args.log_file)
log = command_args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# Creates the corresponding api instance
api = a.get_api_instance(command_args, u.check_dir(session_file))
a.get_output_args(api, command_args, command_args.resume)
a.attribute_args(command_args)
if not command_args.project_id and command_args.name:
command_args.project = command_args.name
if command_args.project:
# create project
pp.project_processing(
api, command_args, command_args.resume, session_file=session_file,
path=path, log=log, create=True)
if command_args.project_id and (
command_args.project_attributes or
command_args.name or command_args.tag or command_args.description
or command_args.category):
# update project's attributes
pp.update_project(command_args, api, command_args.resume, \
session_file=session_file)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir, log_file=session_file,
verbosity=command_args.verbosity)
def reify_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different processing functions
"""
command = command_handling(args, COMMAND_LOG)
# Parses command line arguments.
command_args = a.parse_and_check(command)
if command_args.resume:
command_args, session_file, _ = get_stored_command(
args,
command_args.debug,
command_log=COMMAND_LOG,
dirs_log=DIRS_LOG,
sessions_log=SESSIONS_LOG)
if command_args.output is None:
command_args.output = os.path.join(command_args.output_dir,
DEFAULT_OUTPUT)
else:
if command_args.output_dir is None:
command_args.output_dir = a.NOW
if command_args.output is None:
command_args.output = os.path.join(command_args.output_dir,
DEFAULT_OUTPUT)
if len(os.path.dirname(command_args.output).strip()) == 0:
command_args.output = os.path.join(command_args.output_dir,
command_args.output)
directory = u.check_dir(command_args.output)
command_args.output_dir = directory
session_file = os.path.join(directory, SESSIONS_LOG)
u.log_message(command.command + "\n", log_file=session_file)
directory = u.check_dir(os.path.join(command_args.output_dir, "tmp"))
session_file = os.path.join(directory, SESSIONS_LOG)
u.log_message(command.command + "\n", log_file=session_file)
try:
shutil.copy(DEFAULTS_FILE, os.path.join(directory, DEFAULTS_FILE))
except IOError:
pass
u.sys_log_message(u"%s\n" % os.path.abspath(directory),
log_file=DIRS_LOG)
# If --clear-logs the log files are cleared
if "--clear-logs" in args:
clear_log_files(LOG_FILES)
def logger(message):
"""Partial to log messages according to args.verbosity
"""
u.log_message(u.dated(message), \
log_file=session_file, console=command_args.verbosity)
# Creates the corresponding api instance
api = a.get_api_instance(command_args, u.check_dir(session_file))
message = "Starting reification for %s\n\n" % command_args.resource_id
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
reify_resources(command_args, api, logger)
message = "\nReification complete. See the results in %s\n\n" % \
command_args.output
u.log_message(message, \
log_file=session_file, console=command_args.verbosity)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir,
log_file=session_file,
verbosity=command_args.verbosity)
def compute_output(api, args):
""" Creates one or more anomaly detectors using the `training_set`
or uses the ids of previously created BigML models to make
predictions for the `test_set`.
"""
anomaly = None
anomalies = None
# no multi-label support at present
# variables from command-line options
resume = args.resume_
anomaly_ids = args.anomaly_ids_
output = args.predictions
# there's only one anomaly detector to be generated at present
args.max_parallel_anomalies = 1
# anomalies cannot be published yet.
args.public_anomaly = False
# It is compulsory to have a description to publish either datasets or
# anomalies
if (not args.description_ and (args.public_anomaly or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(_, datasets, test_dataset, resume,
csv_properties, fields) = dataset_properties
if args.anomaly_file:
# anomaly is retrieved from the contents of the given local JSON file
anomaly, csv_properties, fields = u.read_local_resource(
args.anomaly_file,
csv_properties=csv_properties)
anomalies = [anomaly]
anomaly_ids = [anomaly['resource']]
else:
# anomaly is retrieved from the remote object
anomalies, anomaly_ids, resume = pa.anomalies_processing(
datasets, anomalies, anomaly_ids, api, args, resume, fields=fields,
session_file=session_file, path=path, log=log)
if anomalies:
anomaly = anomalies[0]
# We update the anomaly's public state if needed
if anomaly:
if not a.has_test(args) and not args.anomalies_dataset:
query_string = MINIMUM_MODEL
elif not a.has_test(args):
query_string = ";".join([EXCLUDE_TREES, r.ALL_FIELDS_QS])
else:
query_string = r.ALL_FIELDS_QS
try:
anomaly_id = anomaly.get('resource', anomaly)
except AttributeError:
anomaly_id = anomaly
anomaly = u.check_resource(anomaly_id,
query_string=query_string,
api=api)
anomalies[0] = anomaly
if (args.public_anomaly or
(args.shared_flag and r.shared_changed(args.shared, anomaly))):
anomaly_args = {}
if args.shared_flag and r.shared_changed(args.shared, anomaly):
anomaly_args.update(shared=args.shared)
if args.public_anomaly:
anomaly_args.update(r.set_publish_anomaly_args(args))
if anomaly_args:
anomaly = r.update_anomaly(anomaly, anomaly_args, args,
api=api, path=path,
session_file=session_file)
anomalies[0] = anomaly
# We get the fields of the anomaly detector if we haven't got
# them yet and need them
if anomaly and (args.test_set or args.export_fields):
fields = pa.get_anomaly_fields(anomaly, csv_properties, args)
# If creating a top anomalies excluded/included dataset
if args.anomalies_dataset and anomaly:
origin_dataset = anomaly['object'].get('dataset')
if origin_dataset is None:
sys.exit("The dataset used to generate the anomaly detector "
"cannot be found. Failed to generate the anomalies "
" dataset.")
local_anomaly = Anomaly(anomaly)
include = args.anomalies_dataset == ANOMALIES_IN
args.anomaly_filter_ = local_anomaly.anomalies_filter(include=include)
_, resume = pd.create_new_dataset(
origin_dataset, api, args, resume, fields=fields,
session_file=session_file, path=path, log=log)
# If predicting
if anomaly and args.score:
args.test_dataset = anomaly['object']['dataset']
if anomalies and (a.has_test(args) or (test_dataset and args.remote)):
# test dataset can be defined by --test-split or --test-dataset or
# --test-datasets
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote anomaly scores: scores are computed as batch anomaly scores
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api, args, resume, name=test_name,
session_file=session_file, path=path, log=log)
(test_source, resume,
csv_properties, test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source, "test", dataset_args, api, args,
resume, session_file=session_file, path=path, log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
test_fields = pd.get_fields_structure(test_dataset,
csv_properties)
batch_anomaly_score_args = r.set_batch_anomaly_score_args(
args, fields=fields,
dataset_fields=test_fields)
remote_anomaly_score(anomaly, test_dataset,
batch_anomaly_score_args, args,
api, resume, prediction_file=output,
session_file=session_file, path=path, log=log)
else:
anomaly_score(anomalies, fields, args, session_file=session_file)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates a sample based on a `train_set`, source or dataset.
"""
samples = None
# variables from command-line options
resume = args.resume_
sample_ids = args.sample_ids_
output = args.predictions
# there's only one sample to be generated at present
args.max_parallel_clusters = 1
# sample cannot be published yet.
args.public_sample = False
# It is compulsory to have a description to publish either datasets or
# clusters
if (not args.description_ and (args.public_sample or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-sample step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-sample step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(_, datasets, _, resume,
csv_properties, fields) = dataset_properties
if args.sample_file:
# sample is retrieved from the contents of the given local JSON file
sample, csv_properties, fields = u.read_local_resource(
args.sample_file,
csv_properties=csv_properties)
samples = [sample]
sample_ids = [sample['resource']]
else:
# sample is retrieved from the remote object
samples, sample_ids, resume = psa.samples_processing(
datasets, samples, sample_ids, api, args, resume,
session_file=session_file, path=path, log=log)
if samples:
sample = samples[0]
# We update the sample's public state if needed
if sample:
if isinstance(sample, basestring):
# build the query string from the sample options
sample = u.check_resource(sample, api.get_sample)
samples[0] = sample
if (args.public_sample or
(args.shared_flag and r.shared_changed(args.shared, sample))):
sample_args = {}
if args.shared_flag and r.shared_changed(args.shared, sample):
sample_args.update(shared=args.shared)
if args.public_sample:
sample_args.update(r.set_publish_sample_args(args))
if sample_args:
sample = r.update_sample(sample, sample_args, args,
api=api, path=path,
session_file=session_file)
samples[0] = sample
# We get the fields of the sample if we haven't got
# them yet and need them
if sample and psa.needs_sample_fields(args):
fields = psa.get_sample_fields(sample, csv_properties, args)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
sample_file(samples[0], fields, args, api, path=path,
session_file=session_file)
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def delete_resources(command_args, api, deleted_list=None):
"""Deletes the resources selected by the user given options
"""
if deleted_list is None:
deleted_list = []
if command_args.output_dir is None:
path = a.NOW
else:
path = command_args.output_dir
session_file = os.path.join(path, SESSIONS_LOG)
message = u.dated("Retrieving objects to delete.\n")
u.log_message(message, log_file=session_file,
console=command_args.verbosity)
# Parses resource types to filter
if command_args.resource_types is not None:
resource_types = [resource_type.strip() for resource_type in
command_args.resource_types.split(',')]
command_args.resource_types_ = resource_types
else:
command_args.resource_types_ = None
delete_list = []
# by ids
if command_args.delete_list:
delete_list = [resource_id.strip() for resource_id in
command_args.delete_list.split(',')]
# in file
if command_args.delete_file:
if not os.path.exists(command_args.delete_file):
sys.exit("File %s not found" % command_args.delete_file)
with open(command_args.delete_file, "r") as delete_file:
resource_id = bigml.api.get_resource_id(
delete_file.readline().strip())
if resource_id:
delete_list.append(resource_id)
# from directory
if command_args.from_dir:
delete_list.extend(retrieve_resources(command_args.from_dir))
# filter resource_types if any
delete_list = filter_resource_types(delete_list,
command_args.resource_types_)
# by time interval and tag (plus filtered resource_types)
time_qs_list = time_interval_qs(command_args, api)
delete_list.extend(get_delete_list(command_args, api, time_qs_list))
# by filter expression (plus filtered resource_types)
filter_qs_list = filter_qs(command_args, api)
delete_list.extend(get_delete_list(command_args, api, filter_qs_list))
delete_list = [resource_id for resource_id in delete_list \
if resource_id not in deleted_list]
# if there are projects or executions, delete them first
bulk_deletion = not command_args.dry_run and \
any([resource_id.startswith("project/") or \
(not command_args.execution_only and \
resource_id.startswith("execution/")) for resource_id in delete_list])
aprox = "*" if bulk_deletion else ""
# if bulk_deletion, keep only the project and executions resources in
# the deletion list
types_summary, delete_list = resources_by_type( \
delete_list, bulk_deletion)
message = u.dated("Deleting %s objects%s.\n" % (len(delete_list), aprox))
u.log_message(message, log_file=session_file,
console=command_args.verbosity)
for resource_type, instances in types_summary.items():
message = "%s%ss: %s\n" % (" " * INDENT_IDS, resource_type,
instances)
u.log_message(message, log_file=session_file,
console=command_args.verbosity)
if aprox != "":
message = ("* WARNING: Deleting a project or an execution will delete"
" also its associated resources. Note that their IDs"
" may not be listed in this report.\n")
u.log_message(message, log_file=session_file,
console=command_args.verbosity)
if len(delete_list) > ROWS_LIMIT:
pre_indent = INDENT_IDS - 4
message = ("\n%s%s\n" % ((" " * pre_indent),
("Showing only the first %s resources.\n%s"
"See details in bigmler_sessions"
" file.\n") % (ROWS_LIMIT,
" " * pre_indent)))
u.log_message(message, log_file=None,
console=command_args.verbosity)
# ensure uniqueness
delete_list = list(set(delete_list))
# Partial console message. Limited number of rows
segment = delete_list[0: ROWS_LIMIT]
message = ("\n%s" % (" " * INDENT_IDS)).join(segment)
message = ("%s" % (" " * INDENT_IDS)) + message + "\n"
u.log_message(message, log_file=None,
console=command_args.verbosity)
# Complete message in session file
message = ("\n%s" % (" " * INDENT_IDS)).join(delete_list)
message = ("%s" % (" " * INDENT_IDS)) + message + "\n"
u.log_message(message, log_file=session_file)
if not command_args.dry_run:
u.delete(api, delete_list, exe_outputs=not command_args.execution_only)
if bulk_deletion:
# if projects and executions have already been deleted, delete the rest
delete_resources(command_args, api, deleted_list=delete_list)
else:
u.print_generated_files(path, log_file=session_file,
verbosity=command_args.verbosity)
def delete_resources(command_args, api):
"""Deletes the resources selected by the user given options
"""
if command_args.output_dir is None:
path = a.NOW
else:
path = command_args.output_dir
session_file = os.path.join(path, SESSIONS_LOG)
message = u.dated("Retrieving objects to delete.\n")
u.log_message(message,
log_file=session_file,
console=command_args.verbosity)
# Parses resource types to filter
if command_args.resource_types is not None:
resource_types = [
resource_type.strip()
for resource_type in command_args.resource_types.split(',')
]
command_args.resource_types_ = resource_types
else:
command_args.resource_types_ = None
delete_list = []
# by ids
if command_args.delete_list:
delete_list = [
resource_id.strip()
for resource_id in command_args.delete_list.split(',')
]
# in file
if command_args.delete_file:
if not os.path.exists(command_args.delete_file):
sys.exit("File %s not found" % command_args.delete_file)
with open(command_args.delete_file, "r") as delete_file:
resource_id = bigml.api.get_resource_id(
delete_file.readline().strip())
if resource_id:
delete_list.append(resource_id)
# from directory
if command_args.from_dir:
delete_list.extend(retrieve_resources(command_args.from_dir))
# filter resource_types if any
delete_list = filter_resource_types(delete_list,
command_args.resource_types_)
# by time interval and tag (plus filtered resource_types)
time_qs_list = time_interval_qs(command_args, api)
delete_list.extend(get_delete_list(command_args, api, time_qs_list))
types_summary = resources_by_type(delete_list)
message = u.dated("Deleting %s objects.\n" % len(delete_list))
u.log_message(message,
log_file=session_file,
console=command_args.verbosity)
for resource_type, instances in types_summary.items():
message = "%s%ss: %s\n" % (" " * INDENT_IDS, resource_type, instances)
u.log_message(message,
log_file=session_file,
console=command_args.verbosity)
if len(delete_list) > ROWS_LIMIT:
pre_indent = INDENT_IDS - 4
message = ("\n%s%s\n" %
((" " * pre_indent),
("Showing only the first %s resources.\n%s"
"See details in bigmler_sessions"
" file.\n") % (ROWS_LIMIT, " " * pre_indent)))
u.log_message(message, log_file=None, console=command_args.verbosity)
# Partial console message. Limited number of rows
segment = delete_list[0:ROWS_LIMIT]
message = ("\n%s" % (" " * INDENT_IDS)).join(segment)
message = ("%s" % (" " * INDENT_IDS)) + message + "\n"
u.log_message(message, log_file=None, console=command_args.verbosity)
# Complete message in session file
message = ("\n%s" % (" " * INDENT_IDS)).join(delete_list)
message = ("%s" % (" " * INDENT_IDS)) + message + "\n"
u.log_message(message, log_file=session_file)
if not command_args.dry_run:
u.delete(api, delete_list)
u.print_generated_files(path,
log_file=session_file,
verbosity=command_args.verbosity)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
pca = None
# variables from command-line options
resume = args.resume_
pca_ids = args.pca_ids_
output = args.projections
# there's only one pca to be generated at present
args.max_parallel_pcas = 1
# pca cannot be published yet.
args.public_pca = False
# It is compulsory to have a description to publish either datasets or
# pcas
if (not args.description_ and (args.public_pca or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
if args.objective_field:
csv_properties.update({'objective_field': args.objective_field})
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(_, datasets, test_dataset,
resume, csv_properties, fields) = dataset_properties
if args.pca_file:
# pca regression is retrieved from the contents of the given local
# JSON file
pca, csv_properties, fields = u.read_local_resource(
args.pca_file,
csv_properties=csv_properties)
pac_ids = [pca]
else:
# pca is retrieved from the remote object or created
pca, resume = \
pc.pca_processing( \
datasets, pca, pca_ids, \
api, args, resume, fields=fields, \
session_file=session_file, path=path, log=log)
# We update the pca public state if needed
if pca:
if isinstance(pca, basestring):
if not a.has_test(args):
query_string = MINIMUM_MODEL
elif args.export_fields:
query_string = r.ALL_FIELDS_QS
else:
query_string = ''
pca = u.check_resource(pca,
api.get_pca,
query_string=query_string)
if (args.public_pca or
(args.shared_flag and r.shared_changed(args.shared,
pca))):
pca_args = {}
if args.shared_flag and r.shared_changed(args.shared,
pca):
pca_args.update(shared=args.shared)
if args.public_pca:
pca_args.update( \
r.set_publish_pca_args(args))
if pca_args:
pca = r.update_pca( \
pca, pca_args, args,
api=api, path=path, \
session_file=session_file)
# We get the fields of the pca if we haven't got
# them yet and need them
if pca and (args.test_set or args.export_fields):
fields = pc.get_pca_fields( \
pca, csv_properties, args)
if fields and args.export_fields:
fields.summary_csv(os.path.join(path, args.export_fields))
# If predicting
if pca and (a.has_test(args) or \
(test_dataset and args.remote)):
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote projections: projections are computed as batch projections
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api, args, resume, name=test_name,
session_file=session_file, path=path, log=log)
(test_source, resume,
csv_properties, test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source, "test", dataset_args, api, args,
resume, session_file=session_file, path=path, log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
csv_properties.update(objective_field=None,
objective_field_present=False)
test_fields = pd.get_fields_structure(test_dataset,
csv_properties)
batch_projection_args = r.set_batch_projection_args(
args, fields=fields,
dataset_fields=test_fields)
remote_projection(pca, test_dataset, \
batch_projection_args, args, \
api, resume, projection_file=output, \
session_file=session_file, path=path, log=log)
else:
projection(pca, fields, args,
session_file=session_file)
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def delete_resources(command_args, api, deleted_list=None):
"""Deletes the resources selected by the user given options
"""
if deleted_list is None:
deleted_list = []
if command_args.output_dir is None:
path = a.NOW
else:
path = command_args.output_dir
session_file = os.path.join(path, SESSIONS_LOG)
message = u.dated("Retrieving objects to delete.\n")
u.log_message(message,
log_file=session_file,
console=command_args.verbosity)
# Parses resource types to filter
if command_args.resource_types is not None:
resource_types = [
resource_type.strip()
for resource_type in command_args.resource_types.split(',')
]
command_args.resource_types_ = resource_types
else:
command_args.resource_types_ = None
delete_list = []
# by ids
if command_args.delete_list:
delete_list = [
resource_id.strip()
for resource_id in command_args.delete_list.split(',')
]
# in file
if command_args.delete_file:
if not os.path.exists(command_args.delete_file):
sys.exit("File %s not found" % command_args.delete_file)
with open(command_args.delete_file, "r") as delete_file:
resource_id = bigml.api.get_resource_id(
delete_file.readline().strip())
if resource_id:
delete_list.append(resource_id)
# from directory
if command_args.from_dir:
delete_list.extend(retrieve_resources(command_args.from_dir))
# filter resource_types if any
delete_list = filter_resource_types(delete_list,
command_args.resource_types_)
# by time interval and tag (plus filtered resource_types)
time_qs_list = time_interval_qs(command_args, api)
delete_list.extend(get_delete_list(command_args, api, time_qs_list))
# by filter expression (plus filtered resource_types)
filter_qs_list = filter_qs(command_args)
delete_list.extend(get_delete_list(command_args, api, filter_qs_list))
delete_list = [resource_id for resource_id in delete_list \
if resource_id not in deleted_list]
# if there are projects or executions, delete them first
bulk_deletion = not command_args.dry_run and \
any([resource_id.startswith("project/") or \
(not command_args.execution_only and \
resource_id.startswith("execution/")) for resource_id in delete_list])
aprox = "*" if bulk_deletion else ""
# if bulk_deletion, keep only the project and executions resources in
# the deletion list
types_summary, delete_list = resources_by_type( \
delete_list, bulk_deletion)
message = u.dated("Deleting %s objects%s.\n" % (len(delete_list), aprox))
u.log_message(message,
log_file=session_file,
console=command_args.verbosity)
for resource_type, instances in types_summary.items():
message = "%s%ss: %s\n" % (" " * INDENT_IDS, resource_type, instances)
u.log_message(message,
log_file=session_file,
console=command_args.verbosity)
if aprox != "":
message = ("* WARNING: Deleting a project or an execution will delete"
" also its associated resources. Note that their IDs"
" may not be listed in this report.\n")
u.log_message(message,
log_file=session_file,
console=command_args.verbosity)
if len(delete_list) > ROWS_LIMIT:
pre_indent = INDENT_IDS - 4
message = ("\n%s%s\n" %
((" " * pre_indent),
("Showing only the first %s resources.\n%s"
"See details in bigmler_sessions"
" file.\n") % (ROWS_LIMIT, " " * pre_indent)))
u.log_message(message, log_file=None, console=command_args.verbosity)
# ensure uniqueness
delete_list = list(set(delete_list))
# Partial console message. Limited number of rows
segment = delete_list[0:ROWS_LIMIT]
message = ("\n%s" % (" " * INDENT_IDS)).join(segment)
message = ("%s" % (" " * INDENT_IDS)) + message + "\n"
u.log_message(message, log_file=None, console=command_args.verbosity)
# Complete message in session file
message = ("\n%s" % (" " * INDENT_IDS)).join(delete_list)
message = ("%s" % (" " * INDENT_IDS)) + message + "\n"
u.log_message(message, log_file=session_file)
if not command_args.dry_run:
u.delete(api, delete_list, exe_outputs=not command_args.execution_only)
if bulk_deletion:
# if projects and executions have already been deleted, delete the rest
delete_resources(command_args, api, deleted_list=delete_list)
else:
u.print_generated_files(path,
log_file=session_file,
verbosity=command_args.verbosity)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
topic_model = None
topic_models = None
# no multi-label support at present
# variables from command-line options
resume = args.resume_
topic_model_ids = args.topic_model_ids_
output = args.predictions
# there's only one topic model resource to be generated at present
args.max_parallel_topic_models = 1
# topic models cannot be published yet.
args.public_topic_model = False
# It is compulsory to have a description to publish either datasets or
# topic models
if (not args.description_ and (args.public_topic_model or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(_, datasets, test_dataset,
resume, csv_properties, fields) = dataset_properties
if args.topic_model_file:
# topic model is retrieved from the contents of the given local JSON
# file
topic_model, csv_properties, fields = u.read_local_resource(
args.topic_model_file,
csv_properties=csv_properties)
topic_models = [topic_model]
topic_model_ids = [topic_model['resource']]
else:
# topic model is retrieved from the remote object
topic_models, topic_model_ids, resume = pt.topic_model_processing(
datasets, topic_models, topic_model_ids, api, args, resume,
fields=fields,
session_file=session_file, path=path, log=log)
if topic_models:
topic_model = topic_models[0]
# We update the topic model's public state if needed
if topic_model:
if isinstance(topic_model, basestring):
if not a.has_test(args):
query_string = MINIMUM_MODEL
else:
query_string = ''
topic_model = u.check_resource(topic_model, api.topic_model,
query_string=query_string)
topic_models[0] = topic_model
if (args.public_topic_model or
(args.shared_flag and
r.shared_changed(args.shared, topic_model))):
topic_model_args = {}
if args.shared_flag and \
r.shared_changed(args.shared, topic_model):
topic_model_args.update(shared=args.shared)
if args.public_topic_model:
topic_model_args.update(r.set_publish_topic_model_args(args))
if topic_model_args:
topic_model = r.update_topic_model( \
topic_model, topic_model_args, args,
api=api, path=path,
session_file=session_file)
topic_models[0] = topic_model
# We get the fields of the topic model if we haven't got
# them yet and need them
if topic_model and args.test_set:
csv_properties.update({'objective_field_present': False,
'objective_field': None})
fields = pt.get_topic_model_fields(topic_model, csv_properties, args)
# If predicting
if topic_models and (a.has_test(args) or (test_dataset and args.remote)):
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote topic distributions:topic distributions are computed as
# batch topic distributions
# in bigml.com except when --no-batch flag is set.
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api, args, resume, name=test_name,
session_file=session_file, path=path, log=log)
(test_source, resume,
csv_properties, test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source, "test", dataset_args, api, args,
resume, session_file=session_file, path=path, log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
test_fields = pd.get_fields_structure(test_dataset,
csv_properties)
batch_topic_distribution_args = \
r.set_batch_topic_distribution_args( \
args, fields=fields, \
dataset_fields=test_fields)
remote_topic_distribution( \
topic_model, test_dataset, batch_topic_distribution_args,
args, api, resume, prediction_file=output,
session_file=session_file, path=path, log=log)
else:
topic_distribution(topic_models, fields, args,
session_file=session_file)
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
cluster = None
clusters = None
# no multi-label support at present
# variables from command-line options
resume = args.resume_
cluster_ids = args.cluster_ids_
output = args.predictions
# there's only one cluster to be generated at present
args.max_parallel_clusters = 1
# clusters cannot be published yet.
args.public_cluster = False
# It is compulsory to have a description to publish either datasets or
# clusters
if (not args.description_ and (args.public_cluster or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(_, datasets, test_dataset,
resume, csv_properties, fields) = dataset_properties
if args.cluster_file:
# cluster is retrieved from the contents of the given local JSON file
cluster, csv_properties, fields = u.read_local_resource(
args.cluster_file,
csv_properties=csv_properties)
clusters = [cluster]
cluster_ids = [cluster['resource']]
else:
# cluster is retrieved from the remote object
clusters, cluster_ids, resume = pc.clusters_processing(
datasets, clusters, cluster_ids, api, args, resume, fields=fields,
session_file=session_file, path=path, log=log)
if clusters:
cluster = clusters[0]
# We update the cluster's public state if needed
if cluster:
if isinstance(cluster, basestring):
if args.cluster_datasets is None and not a.has_test(args):
query_string = MINIMUM_MODEL
else:
query_string = ''
cluster = u.check_resource(cluster, api.get_cluster,
query_string=query_string)
clusters[0] = cluster
if (args.public_cluster or
(args.shared_flag and r.shared_changed(args.shared, cluster))):
cluster_args = {}
if args.shared_flag and r.shared_changed(args.shared, cluster):
cluster_args.update(shared=args.shared)
if args.public_cluster:
cluster_args.update(r.set_publish_cluster_args(args))
if cluster_args:
cluster = r.update_cluster(cluster, cluster_args, args,
api=api, path=path,
session_file=session_file)
clusters[0] = cluster
# We get the fields of the cluster if we haven't got
# them yet and need them
if cluster and args.test_set:
fields = pc.get_cluster_fields(cluster, csv_properties, args)
# If predicting
if clusters and (a.has_test(args) or (test_dataset and args.remote)):
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote centroids: centroids are computed as batch centroids
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api, args, resume, name=test_name,
session_file=session_file, path=path, log=log)
(test_source, resume,
csv_properties, test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source, "test", dataset_args, api, args,
resume, session_file=session_file, path=path, log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
test_fields = pd.get_fields_structure(test_dataset,
csv_properties)
batch_centroid_args = r.set_batch_centroid_args(
args, fields=fields,
dataset_fields=test_fields)
remote_centroid(cluster, test_dataset, batch_centroid_args, args,
api, resume, prediction_file=output,
session_file=session_file, path=path, log=log)
else:
centroid(clusters, fields, args, session_file=session_file)
if cluster and args.cluster_datasets is not None:
centroids_info = cluster['object']['clusters']['clusters']
centroids = {centroid['name']: centroid['id']
for centroid in centroids_info}
datasets = cluster['object']['cluster_datasets']
if args.cluster_datasets == '':
centroid_ids = centroids.values()
else:
centroid_ids = [centroids[cluster_name] for cluster_name in
args.cluster_datasets_
if datasets[centroids[cluster_name]] == '']
for centroid_id in centroid_ids:
dataset_args = {'centroid': centroid_id}
r.create_dataset(cluster, dataset_args, args, api=api, path=path,
session_file=session_file, log=log,
dataset_type='cluster')
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def delete_resources(command_args, api):
"""Deletes the resources selected by the user given options
"""
if command_args.output_dir is None:
path = a.NOW
else:
path = command_args.output_dir
session_file = os.path.join(path, SESSIONS_LOG)
message = u.dated("Retrieving objects to delete.\n")
u.log_message(message, log_file=session_file,
console=command_args.verbosity)
# Parses resource types to filter
if command_args.resource_types is not None:
resource_types = [resource_type.strip() for resource_type in
command_args.resource_types.split(',')]
command_args.resource_types_ = resource_types
else:
command_args.resource_types_ = None
delete_list = []
# by ids
if command_args.delete_list:
delete_list = [resource_id.strip() for resource_id in
command_args.delete_list.split(',')]
# in file
if command_args.delete_file:
if not os.path.exists(command_args.delete_file):
sys.exit("File %s not found" % command_args.delete_file)
with open(command_args.delete_file, "r") as delete_file:
resource_id = bigml.api.get_resource_id(
delete_file.readline().strip())
if resource_id:
delete_list.append(resource_id)
# from directory
if command_args.from_dir:
delete_list.extend(retrieve_resources(command_args.from_dir))
# filter resource_types if any
delete_list = filter_resource_types(delete_list,
command_args.resource_types_)
# by time interval and tag (plus filtered resource_types)
time_qs_list = time_interval_qs(command_args, api)
delete_list.extend(get_delete_list(command_args, api, time_qs_list))
types_summary = resources_by_type(delete_list)
message = u.dated("Deleting %s objects.\n" % len(delete_list))
u.log_message(message, log_file=session_file,
console=command_args.verbosity)
for resource_type, instances in types_summary.items():
message = "%s%ss: %s\n" % (" " * INDENT_IDS, resource_type,
instances)
u.log_message(message, log_file=session_file,
console=command_args.verbosity)
if len(delete_list) > ROWS_LIMIT:
pre_indent = INDENT_IDS - 4
message = ("\n%s%s\n" % ((" " * pre_indent),
("Showing only the first %s resources.\n%s"
"See details in bigmler_sessions"
" file.\n") % (ROWS_LIMIT,
" " * pre_indent)))
u.log_message(message, log_file=None,
console=command_args.verbosity)
# Partial console message. Limited number of rows
segment = delete_list[0: ROWS_LIMIT]
message = ("\n%s" % (" " * INDENT_IDS)).join(segment)
message = ("%s" % (" " * INDENT_IDS)) + message + "\n"
u.log_message(message, log_file=None,
console=command_args.verbosity)
# Complete message in session file
message = ("\n%s" % (" " * INDENT_IDS)).join(delete_list)
message = ("%s" % (" " * INDENT_IDS)) + message + "\n"
u.log_message(message, log_file=session_file)
if not command_args.dry_run:
u.delete(api, delete_list)
u.print_generated_files(path, log_file=session_file,
verbosity=command_args.verbosity)
def project_dispatcher(args=sys.argv[1:]):
"""Parses command line and calls the different processing functions
"""
command = command_handling(args, COMMAND_LOG)
# Parses command line arguments.
command_args = a.parse_and_check(command)
if command_args.resume:
command_args, session_file, _ = get_stored_command(
args,
command_args.debug,
command_log=COMMAND_LOG,
dirs_log=DIRS_LOG,
sessions_log=SESSIONS_LOG)
else:
if command_args.output_dir is None:
command_args.output_dir = a.NOW
directory = u.check_dir("%s/x.txt" % command_args.output_dir)
command_args.output_dir = directory
session_file = os.path.join(directory, SESSIONS_LOG)
u.log_message(command.command + "\n", log_file=session_file)
directory = u.check_dir(os.path.join(command_args.output_dir, "tmp"))
session_file = os.path.join(directory, SESSIONS_LOG)
u.log_message(command.command + "\n", log_file=session_file)
try:
shutil.copy(DEFAULTS_FILE, os.path.join(directory, DEFAULTS_FILE))
except IOError:
pass
u.sys_log_message(u"%s\n" % os.path.abspath(directory),
log_file=DIRS_LOG)
path = u.check_dir("%s/x.txt" % command_args.output_dir)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
# If logging is required set the file for logging
log = None
if command_args.log_file:
u.check_dir(command_args.log_file)
log = command_args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# Creates the corresponding api instance
api = a.get_api_instance(command_args, u.check_dir(session_file))
a.get_output_args(api, command_args, command_args.resume)
a.attribute_args(command_args)
if not command_args.project_id and command_args.name:
command_args.project = command_args.name
if command_args.project:
# create project
pp.project_processing(api,
command_args,
command_args.resume,
session_file=session_file,
path=path,
log=log,
create=True)
if command_args.project_id and (command_args.project_attributes
or command_args.name or command_args.tag
or command_args.description
or command_args.category):
# update project's attributes
pp.update_project(command_args, api, command_args.resume, \
session_file=session_file)
u.log_message("_" * 80 + "\n", log_file=session_file)
u.print_generated_files(command_args.output_dir,
log_file=session_file,
verbosity=command_args.verbosity)
def compute_output(api, args):
""" Creates one or more models using the `training_set` or uses the ids
of previously created BigML models to make predictions for the `test_set`.
"""
association = None
associations = None
# no multi-label support at present
# variables from command-line options
resume = args.resume_
association_ids = args.association_ids_
output = args.predictions
# there's only one association resource to be generated at present
args.max_parallel_associations = 1
# associations cannot be published yet.
args.public_association = False
# It is compulsory to have a description to publish either datasets or
# associations
if (not args.description_ and (args.public_association or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(_, datasets, test_dataset,
resume, csv_properties, fields) = dataset_properties
if args.association_file:
# association is retrieved from the contents of the given local JSON
# file
association, csv_properties, fields = u.read_local_resource(
args.association_file,
csv_properties=csv_properties)
associations = [association]
association_ids = [association['resource']]
else:
# association is retrieved from the remote object
associations, association_ids, resume = pa.associations_processing(
datasets, associations, association_ids, api, args, resume,
fields=fields,
session_file=session_file, path=path, log=log)
if associations:
association = associations[0]
# We update the association's public state if needed
if association:
if isinstance(association, basestring):
if not a.has_test(args):
query_string = MINIMUM_MODEL
else:
query_string = ''
association = u.check_resource(association, api.get_association,
query_string=query_string)
associations[0] = association
if (args.public_association or
(args.shared_flag and
r.shared_changed(args.shared, association))):
association_args = {}
if args.shared_flag and \
r.shared_changed(args.shared, association):
association_args.update(shared=args.shared)
if args.public_association:
association_args.update(r.set_publish_association_args(args))
if association_args:
association = r.update_association( \
association, association_args, args,
api=api, path=path,
session_file=session_file)
associations[0] = association
# We get the fields of the association if we haven't got
# them yet and need them
if association and args.test_set:
fields = pa.get_association_fields(association, csv_properties, args)
# If predicting
if associations and (a.has_test(args) or (test_dataset and args.remote)):
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote association sets: association sets are computed as
# batch association sets
# in bigml.com except when --no-batch flag is set. They are currently
# not supported yet
if args.remote and not args.no_batch:
sys.exit("Batch association sets are currently not supported.")
"""
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api, args, resume, name=test_name,
session_file=session_file, path=path, log=log)
(test_source, resume,
csv_properties, test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source, "test", dataset_args, api, args,
resume, session_file=session_file, path=path, log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
test_fields = pd.get_fields_structure(test_dataset,
csv_properties)
batch_association_args = r.set_batch_association_args(
args, fields=fields,
dataset_fields=test_fields)
remote_association( \
association, test_dataset, batch_association_args,
args, api, resume, prediction_file=output,
session_file=session_file, path=path, log=log)
"""
else:
sys.exit("Local prediction of association sets is currently"
" not supported.")
"""
association_set(associations, fields, args,
session_file=session_file)
"""
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
dataset_fields = pd.get_fields_structure(dataset, None)
models_or_ensembles = ensemble_ids if ensemble_ids != [] else models
resume = evaluate(
models_or_ensembles,
[dataset],
api,
args,
resume,
fields=fields,
dataset_fields=dataset_fields,
session_file=session_file,
path=path,
log=log,
labels=labels,
all_labels=all_labels,
objective_field=args.objective_field,
)
# If cross_validation_rate is > 0, create remote evaluations and save
# results in json and human-readable format. Then average the results to
# issue a cross_validation measure set.
if args.cross_validation_rate > 0:
args.sample_rate = 1 - args.cross_validation_rate
cross_validate(models, dataset, fields, api, args, resume, session_file=session_file, path=path, log=log)
u.print_generated_files(path, log_file=session_file, verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)
def compute_output(api, args):
""" Creates one or more anomaly detectors using the `training_set`
or uses the ids of previously created BigML models to make
predictions for the `test_set`.
"""
anomaly = None
anomalies = None
# no multi-label support at present
# variables from command-line options
resume = args.resume_
anomaly_ids = args.anomaly_ids_
output = args.predictions
# there's only one anomaly detector to be generated at present
args.max_parallel_anomalies = 1
# anomalies cannot be published yet.
args.public_anomaly = False
# It is compulsory to have a description to publish either datasets or
# anomalies
if (not args.description_ and (args.public_anomaly or
args.public_dataset)):
sys.exit("You should provide a description to publish.")
# When using --new-fields, it is compulsory to specify also a dataset
# id
if args.new_fields and not args.dataset:
sys.exit("To use --new-fields you must also provide a dataset id"
" to generate the new dataset from it.")
path = u.check_dir(output)
session_file = u"%s%s%s" % (path, os.sep, SESSIONS_LOG)
csv_properties = {}
# If logging is required set the file for logging
log = None
if args.log_file:
u.check_dir(args.log_file)
log = args.log_file
# If --clear_logs the log files are cleared
clear_log_files([log])
# basic pre-model step: creating or retrieving the source related info
source, resume, csv_properties, fields = pms.get_source_info(
api, args, resume, csv_properties, session_file, path, log)
# basic pre-model step: creating or retrieving the dataset related info
dataset_properties = pms.get_dataset_info(
api, args, resume, source,
csv_properties, fields, session_file, path, log)
(dataset, datasets, test_dataset, resume,
csv_properties, fields) = dataset_properties
if args.anomaly_file:
# anomaly is retrieved from the contents of the given local JSON file
anomaly, csv_properties, fields = u.read_local_resource(
args.anomaly_file,
csv_properties=csv_properties)
anomalies = [anomaly]
anomaly_ids = [anomaly['resource']]
else:
# anomaly is retrieved from the remote object
anomalies, anomaly_ids, resume = pa.anomalies_processing(
datasets, anomalies, anomaly_ids, api, args, resume, fields=fields,
session_file=session_file, path=path, log=log)
if anomalies:
anomaly = anomalies[0]
# We update the anomaly's public state if needed
if anomaly:
if not a.has_test(args) and not args.anomalies_dataset:
query_string = MINIMUM_MODEL
elif not a.has_test(args):
query_string = ";".join([EXCLUDE_TREES, r.ALL_FIELDS_QS])
else:
query_string = r.ALL_FIELDS_QS
try:
anomaly_id = anomaly.get('resource', anomaly)
except AttributeError:
anomaly_id = anomaly
anomaly = u.check_resource(anomaly_id,
query_string=query_string,
api=api)
anomalies[0] = anomaly
if (args.public_anomaly or
(args.shared_flag and r.shared_changed(args.shared, anomaly))):
anomaly_args = {}
if args.shared_flag and r.shared_changed(args.shared, anomaly):
anomaly_args.update(shared=args.shared)
if args.public_anomaly:
anomaly_args.update(r.set_publish_anomaly_args(args))
if anomaly_args:
anomaly = r.update_anomaly(anomaly, anomaly_args, args,
api=api, path=path,
session_file=session_file)
anomalies[0] = anomaly
# We get the fields of the anomaly detector if we haven't got
# them yet and need them
if anomaly and args.test_set:
fields = pa.get_anomaly_fields(anomaly, csv_properties, args)
# If creating a top anomalies excluded/included dataset
if args.anomalies_dataset and anomaly:
origin_dataset = anomaly['object'].get('dataset')
if origin_dataset is None:
sys.exit("The dataset used to generate the anomaly detector "
"cannot be found. Failed to generate the anomalies "
" dataset.")
local_anomaly = Anomaly(anomaly)
include = args.anomalies_dataset == ANOMALIES_IN
args._anomaly_filter = local_anomaly.anomalies_filter(include=include)
new_dataset, resume = pd.create_new_dataset(
origin_dataset, api, args, resume, fields=fields,
session_file=session_file, path=path, log=log)
# If predicting
if anomaly and args.score:
args.test_dataset = anomaly['object']['dataset']
if anomalies and (a.has_test(args) or (test_dataset and args.remote)):
# test dataset can be defined by --test-split or --test-dataset or
# --test-datasets
if test_dataset is None:
test_dataset = get_test_dataset(args)
# Remote anomaly scores: scores are computed as batch anomaly scores
# in bigml.com except when --no-batch flag is set on
if args.remote and not args.no_batch:
# create test source from file
test_name = "%s - test" % args.name
if args.test_source is None:
test_properties = ps.test_source_processing(
api, args, resume, name=test_name,
session_file=session_file, path=path, log=log)
(test_source, resume,
csv_properties, test_fields) = test_properties
else:
test_source_id = bigml.api.get_source_id(args.test_source)
test_source = api.check_resource(test_source_id)
if test_dataset is None:
# create test dataset from test source
dataset_args = r.set_basic_dataset_args(args, name=test_name)
test_dataset, resume = pd.alternative_dataset_processing(
test_source, "test", dataset_args, api, args,
resume, session_file=session_file, path=path, log=log)
else:
test_dataset_id = bigml.api.get_dataset_id(test_dataset)
test_dataset = api.check_resource(test_dataset_id)
test_fields = pd.get_fields_structure(test_dataset,
csv_properties)
batch_anomaly_score_args = r.set_batch_anomaly_score_args(
args, fields=fields,
dataset_fields=test_fields)
remote_anomaly_score(anomaly, test_dataset,
batch_anomaly_score_args, args,
api, resume, prediction_file=output,
session_file=session_file, path=path, log=log)
else:
anomaly_score(anomalies, fields, args, session_file=session_file)
u.print_generated_files(path, log_file=session_file,
verbosity=args.verbosity)
if args.reports:
clear_reports(path)
if args.upload:
upload_reports(args.reports, path)