def assess_by_id(body): # noqa: E501
"""assess_by_id
Evaluate FAIRness of a data object based on its identifier # noqa: E501
:param body:
:type body: dict | bytes
:rtype: FAIRResults
"""
if connexion.request.is_json:
debug = True
results = []
body = Body.from_dict(connexion.request.get_json())
identifier = body.object_identifier
debug = body.test_debug
oai = body.oaipmh_endpoint
ft = FAIRCheck(uid=identifier, test_debug=debug, oaipmh=oai)
uid_result, pid_result = ft.check_unique_persistent()
core_metadata_result = ft.check_minimal_metatadata()
content_identifier_included_result = ft.check_content_identifier_included(
)
check_searchable_result = ft.check_searchable()
access_result = ft.check_data_access_level()
formal_metadata_result = ft.check_formal_metadata()
semantic_vocab_result = ft.check_semantic_vocabulary()
relatedresources_result = ft.check_relatedresources()
datacontent_result = ft.check_data_content_metadata()
license_result = ft.check_license()
provenance_result = ft.check_data_provenance()
community_standards_result = ft.check_community_metadatastandards()
fileformat_result = ft.check_data_file_format()
results.append(uid_result)
results.append(pid_result)
results.append(core_metadata_result)
results.append(content_identifier_included_result)
results.append(check_searchable_result)
results.append(access_result)
results.append(formal_metadata_result)
results.append(semantic_vocab_result)
results.append(relatedresources_result)
results.append(datacontent_result)
results.append(license_result)
results.append(provenance_result)
results.append(community_standards_result)
results.append(fileformat_result)
#timestmp = datetime.datetime.now().replace(microsecond=0).isoformat()
timestmp = datetime.datetime.now().replace(microsecond=0).isoformat(
) + "Z" # generate RFC 3339 timestamp as specified in openapi3
metric_spec = Preprocessor.metric_specification
totalmetrics = len(results)
final_response = FAIRResults(timestamp=timestmp,
metric_specification=metric_spec,
total_metrics=totalmetrics,
results=results)
return final_response
def main():
config = ConfigParser.ConfigParser()
my_path = Path(__file__).parent.parent
ini_path = os.path.join(my_path, 'config', 'server.ini')
config.read(ini_path)
YAML_DIR = config['SERVICE']['yaml_directory']
METRIC_YAML = config['SERVICE']['metrics_yaml']
METRIC_YML_PATH = os.path.join(my_path, YAML_DIR, METRIC_YAML)
SPDX_URL = config['EXTERNAL']['spdx_license_github']
DATACITE_API_REPO = config['EXTERNAL']['datacite_api_repo']
RE3DATA_API = config['EXTERNAL']['re3data_api']
METADATACATALOG_API = config['EXTERNAL']['metadata_catalog']
isDebug = config.getboolean('SERVICE', 'debug_mode')
data_files_limit = int(config['SERVICE']['data_files_limit'])
metric_specification = config['SERVICE']['metric_specification']
preproc = Preprocessor()
preproc.retrieve_metrics_yaml(METRIC_YML_PATH, data_files_limit,
metric_specification)
print('Total metrics defined: {}'.format(preproc.get_total_metrics()))
isDebug = config.getboolean('SERVICE', 'debug_mode')
preproc.retrieve_licenses(SPDX_URL, isDebug)
preproc.retrieve_datacite_re3repos(RE3DATA_API, DATACITE_API_REPO, isDebug)
preproc.retrieve_metadata_standards(METADATACATALOG_API, isDebug)
preproc.retrieve_science_file_formats(isDebug)
preproc.retrieve_long_term_file_formats(isDebug)
print('Total SPDX licenses : {}'.format(preproc.get_total_licenses()))
print('Total re3repositories found from datacite api : {}'.format(
len(preproc.getRE3repositories())))
print('Total subjects area of imported metadata standards : {}'.format(
len(preproc.metadata_standards)))
start = False
usedatacite = True
tracemalloc.start()
n = 1
for identifier in testpids:
print(identifier)
print(n)
n += 1
if identifier == startpid or not startpid:
start = True
if start:
ft = FAIRCheck(uid=identifier,
test_debug=debug,
metadata_service_url=metadata_service_endpoint,
metadata_service_type=metadata_service_type,
use_datacite=usedatacite)
#ft = FAIRCheck(uid=identifier, test_debug=True, use_datacite=usedatacite)
uid_result, pid_result = ft.check_unique_persistent()
ft.retrieve_metadata_embedded(ft.extruct_result)
include_embedded = True
if ft.repeat_pid_check:
uid_result, pid_result = ft.check_unique_persistent()
ft.retrieve_metadata_external()
core_metadata_result = ft.check_minimal_metatadata()
content_identifier_included_result = ft.check_content_identifier_included(
)
access_level_result = ft.check_data_access_level()
license_result = ft.check_license()
relatedresources_result = ft.check_relatedresources()
check_searchable_result = ft.check_searchable()
data_content_metadata = ft.check_data_content_metadata()
data_file_format_result = ft.check_data_file_format()
community_standards_result = ft.check_community_metadatastandards()
data_provenance_result = ft.check_data_provenance()
formal_representation_result = ft.check_formal_metadata()
semantic_vocabulary_result = ft.check_semantic_vocabulary()
metadata_preserved_result = ft.check_metadata_preservation()
standard_protocol_metadata_result = ft.check_standardised_protocol_metadata(
)
standard_protocol_data_result = ft.check_standardised_protocol_data(
)
results = [
uid_result, pid_result, core_metadata_result,
content_identifier_included_result, check_searchable_result,
access_level_result, formal_representation_result,
semantic_vocabulary_result, license_result,
data_file_format_result, data_provenance_result,
relatedresources_result, community_standards_result,
data_content_metadata, metadata_preserved_result,
standard_protocol_data_result,
standard_protocol_metadata_result
]
#results=[core_metadata_result,uid_result, pid_result]
#print(ft.metadata_merged)
debug_messages = ft.get_log_messages_dict()
ft.logger_message_stream.flush()
ft.get_assessment_summary(results)
for res_k, res_v in enumerate(results):
if ft.isDebug:
debug_list = debug_messages.get(res_v['metric_identifier'])
#debug_list= ft.msg_filter.getMessage(res_v['metric_identifier'])
if debug_list is not None:
results[res_k]['test_debug'] = debug_messages.get(
res_v['metric_identifier'])
else:
results[res_k]['test_debug'] = [
'INFO: No debug messages received'
]
else:
results[res_k]['test_debug'] = ['INFO: Debugging disabled']
debug_messages = {}
print(json.dumps(results, indent=4, sort_keys=True))
#remove unused logger handlers and filters to avoid memory leaks
ft.logger.handlers = [ft.logger.handlers[-1]]
#ft.logger.filters = [ft.logger.filters]
current, peak = tracemalloc.get_traced_memory()
print(
f"Current memory usage is {current / 10 ** 6}MB; Peak was {peak / 10 ** 6}MB"
)
snapshot = tracemalloc.take_snapshot()
top_stats = snapshot.statistics('traceback')
# pick the biggest memory block
stat = top_stats[0]
print("%s memory blocks: %.1f KiB" %
(stat.count, stat.size / 1024))
for line in stat.traceback.format():
print(line)
for i, stat in enumerate(snapshot.statistics('filename')[:5], 1):
print(i, str(stat))
#preproc.logger.
gc.collect()
tracemalloc.stop()
def main():
config = ConfigParser.ConfigParser()
my_path = Path(__file__).parent.parent
ini_path = os.path.join(my_path,'config','server.ini')
config.read(ini_path)
YAML_DIR = config['SERVICE']['yaml_directory']
METRIC_YAML = config['SERVICE']['metrics_yaml']
METRIC_YML_PATH = os.path.join(my_path, YAML_DIR , METRIC_YAML)
SPDX_URL = config['EXTERNAL']['spdx_license_github']
DATACITE_API_REPO = config['EXTERNAL']['datacite_api_repo']
RE3DATA_API = config['EXTERNAL']['re3data_api']
METADATACATALOG_API = config['EXTERNAL']['metadata_catalog']
isDebug = config.getboolean('SERVICE', 'debug_mode')
data_files_limit = int(config['SERVICE']['data_files_limit'])
metric_specification = config['SERVICE']['metric_specification']
preproc = Preprocessor()
preproc.retrieve_metrics_yaml(METRIC_YML_PATH, data_files_limit,metric_specification)
print('Total metrics defined: {}'.format(preproc.get_total_metrics()))
isDebug = config.getboolean('SERVICE', 'debug_mode')
preproc.retrieve_licenses(SPDX_URL, isDebug)
preproc.retrieve_datacite_re3repos(RE3DATA_API, DATACITE_API_REPO, isDebug)
preproc.retrieve_metadata_standards(METADATACATALOG_API, isDebug)
preproc.retrieve_science_file_formats(isDebug)
preproc.retrieve_long_term_file_formats(isDebug)
print('Total SPDX licenses : {}'.format(preproc.get_total_licenses()))
print('Total re3repositories found from datacite api : {}'.format(len(preproc.getRE3repositories())))
print('Total subjects area of imported metadata standards : {}'.format(len(preproc.metadata_standards)))
start=False
for identifier in testpids:
print (identifier)
if identifier==startpid or not startpid:
start=True
if start:
ft = FAIRCheck(uid=identifier, test_debug=True, use_datacite=False)
uid_result, pid_result = ft.check_unique_persistent()
core_metadata_result = ft.check_minimal_metatadata()
content_identifier_included_result = ft.check_content_identifier_included()
access_level_result=ft.check_data_access_level()
license_result = ft.check_license()
relatedresources_result = ft.check_relatedresources()
check_searchable_result = ft.check_searchable()
data_file_format_result=ft.check_data_file_format()
community_standards_result=ft.check_community_metadatastandards()
data_provenance_result=ft.check_data_provenance()
data_content_metadata = ft.check_data_content_metadata()
formal_representation_result=ft.check_formal_metadata()
semantic_vocabulary_result =ft.check_semantic_vocabulary()
metadata_preserved_result = ft.check_metadata_preservation()
standard_protocol_data_result = ft.check_standardised_protocol_data()
standard_protocol_metadata_result = ft.check_standardised_protocol_metadata()
results = [uid_result, pid_result, core_metadata_result, content_identifier_included_result, check_searchable_result, access_level_result, formal_representation_result,semantic_vocabulary_result, license_result, data_file_format_result,data_provenance_result,relatedresources_result,community_standards_result,data_content_metadata,metadata_preserved_result, standard_protocol_data_result,standard_protocol_metadata_result]
#results=[core_metadata_result,uid_result, pid_result]
#print(ft.metadata_merged)
for res_k, res_v in enumerate(results):
if ft.isDebug:
debug_list= ft.msg_filter.getMessage(res_v['metric_identifier'])
if debug_list is not None:
results[res_k]['test_debug'] = ft.msg_filter.getMessage(res_v['metric_identifier'])
else:
results[res_k]['test_debug'] =['INFO: No debug messages received']
else:
results[res_k]['test_debug'] = ['INFO: Debugging disabled']
print(json.dumps(results, indent=4, sort_keys=True))
def assess_by_id(body): # noqa: E501
"""assess_by_id
Evaluate FAIRness of a data object based on its identifier # noqa: E501
:param body:
:type body: dict | bytes
:rtype: FAIRResults
"""
if connexion.request.is_json:
debug = True
results = []
body = Body.from_dict(connexion.request.get_json())
identifier=body.object_identifier
debug = body.test_debug
oai = body.oaipmh_endpoint
ft = FAIRCheck(uid=identifier, test_debug=debug, oaipmh=oai)
uid_result, pid_result = ft.check_unique_persistent()
core_metadata_result = ft.check_minimal_metatadata()
content_identifier_included_result = ft.check_content_identifier_included()
access_level_result = ft.check_data_access_level()
license_result = ft.check_license()
related_resources_result = ft.check_relatedresources()
check_searchable_result = ft.check_searchable()
data_file_format_result = ft.check_data_file_format()
community_standards_result = ft.check_community_metadatastandards()
data_provenance_result = ft.check_data_provenance()
data_content_result = ft.check_data_content_metadata()
formal_metadata_result = ft.check_formal_metadata()
semantic_vocab_result = ft.check_semantic_vocabulary()
metadata_preserved_result = ft.check_metadata_preservation()
standard_protocol_data_result = ft.check_standardised_protocol_data()
standard_protocol_metadata_result = ft.check_standardised_protocol_metadata()
results.append(uid_result)
results.append(pid_result)
results.append(core_metadata_result)
results.append(content_identifier_included_result)
results.append(check_searchable_result)
results.append(access_level_result)
results.append(formal_metadata_result)
results.append(semantic_vocab_result)
results.append(related_resources_result)
results.append(data_content_result)
results.append(license_result)
results.append(data_provenance_result)
results.append(community_standards_result)
results.append(data_file_format_result)
results.append(standard_protocol_data_result)
results.append(standard_protocol_metadata_result)
for res_k, res_v in enumerate(results):
if ft.isDebug:
debug_list = ft.msg_filter.getMessage(res_v['metric_identifier'])
if debug_list is not None:
results[res_k]['test_debug'] = ft.msg_filter.getMessage(res_v['metric_identifier'])
else:
results[res_k]['test_debug'] = ['INFO: No debug messages received']
timestmp = datetime.datetime.now().replace(microsecond=0).isoformat()
metric_spec = Preprocessor.metric_specification
metric_version = os.path.basename(Preprocessor.METRIC_YML_PATH)
totalmetrics = len(results)
final_response = FAIRResults(timestamp= timestmp, test_id= ft.test_id, metric_version=metric_version, metric_specification=metric_spec, total_metrics=totalmetrics, results=results)
return final_response
def assess_by_id(body): # noqa: E501
"""assess_by_id
Evaluate FAIRness of a data object based on its identifier # noqa: E501
:param body:
:type body: dict | bytes
:rtype: FAIRResults
"""
if connexion.request.is_json:
debug = True
results = []
body = Body.from_dict(connexion.request.get_json())
identifier = body.object_identifier
debug = body.test_debug
metadata_service_endpoint = body.metadata_service_endpoint
oaipmh_endpoint = body.oaipmh_endpoint
metadata_service_type = body.metadata_service_type
usedatacite = body.use_datacite
logger = Preprocessor.logger
logger.info('Assessment target: ' + identifier)
print('Assessment target: ', identifier, flush=True)
ft = FAIRCheck(uid=identifier,
test_debug=debug,
metadata_service_url=metadata_service_endpoint,
metadata_service_type=metadata_service_type,
use_datacite=usedatacite,
oaipmh_endpoint=oaipmh_endpoint)
# set target for remote logging
remote_log_host, remote_log_path = Preprocessor.remote_log_host, Preprocessor.remote_log_path
#print(remote_log_host, remote_log_path)
if remote_log_host and remote_log_path:
ft.set_remote_logging_target(remote_log_host, remote_log_path)
uid_result, pid_result = ft.check_unique_persistent()
ft.retrieve_metadata_embedded(ft.extruct_result)
if ft.repeat_pid_check:
uid_result, pid_result = ft.check_unique_persistent()
include_embedded = True
ft.retrieve_metadata_external()
if ft.repeat_pid_check:
uid_result, pid_result = ft.check_unique_persistent()
core_metadata_result = ft.check_minimal_metatadata()
content_identifier_included_result = ft.check_content_identifier_included(
)
access_level_result = ft.check_data_access_level()
license_result = ft.check_license()
related_resources_result = ft.check_relatedresources()
check_searchable_result = ft.check_searchable()
data_content_result = ft.check_data_content_metadata()
data_file_format_result = ft.check_data_file_format()
community_standards_result = ft.check_community_metadatastandards()
data_provenance_result = ft.check_data_provenance()
formal_metadata_result = ft.check_formal_metadata()
semantic_vocab_result = ft.check_semantic_vocabulary()
metadata_preserved_result = ft.check_metadata_preservation()
standard_protocol_data_result = ft.check_standardised_protocol_data()
standard_protocol_metadata_result = ft.check_standardised_protocol_metadata(
)
results.append(uid_result)
results.append(pid_result)
results.append(core_metadata_result)
results.append(content_identifier_included_result)
results.append(check_searchable_result)
results.append(access_level_result)
results.append(formal_metadata_result)
results.append(semantic_vocab_result)
results.append(related_resources_result)
results.append(data_content_result)
results.append(license_result)
results.append(data_provenance_result)
results.append(community_standards_result)
results.append(data_file_format_result)
results.append(standard_protocol_data_result)
results.append(standard_protocol_metadata_result)
debug_messages = ft.get_log_messages_dict()
ft.logger_message_stream.flush()
summary = ft.get_assessment_summary(results)
for res_k, res_v in enumerate(results):
if ft.isDebug:
debug_list = debug_messages.get(res_v['metric_identifier'])
# debug_list= ft.msg_filter.getMessage(res_v['metric_identifier'])
if debug_list is not None:
results[res_k]['test_debug'] = debug_messages.get(
res_v['metric_identifier'])
else:
results[res_k]['test_debug'] = [
'INFO: No debug messages received'
]
else:
results[res_k]['test_debug'] = ['INFO: Debugging disabled']
debug_messages = {}
ft.logger.handlers = [ft.logger.handlers[-1]]
#timestmp = datetime.datetime.now().replace(microsecond=0).isoformat()
timestmp = datetime.datetime.now().replace(microsecond=0).isoformat(
) + "Z" # use timestamp format from RFC 3339 as specified in openapi3
metric_spec = Preprocessor.metric_specification
metric_version = os.path.basename(Preprocessor.METRIC_YML_PATH)
totalmetrics = len(results)
request = body.to_dict()
if ft.pid_url:
idhelper = IdentifierHelper(ft.pid_url)
request[
'normalized_object_identifier'] = idhelper.get_normalized_id()
final_response = FAIRResults(request=request,
timestamp=timestmp,
software_version=ft.FUJI_VERSION,
test_id=ft.test_id,
metric_version=metric_version,
metric_specification=metric_spec,
total_metrics=totalmetrics,
results=results,
summary=summary)
return final_response