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fair_check.py
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fair_check.py
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# SPDX-FileCopyrightText: 2020 PANGAEA (https://www.pangaea.de/)
#
# SPDX-License-Identifier: MIT
import hashlib
import io
import json
import logging
import logging.handlers
import re
from urllib.parse import urlparse
import pandas as pd
from fuji_server import __version__
from fuji_server.evaluators.fair_evaluator_api import FAIREvaluatorAPI
from fuji_server.evaluators.fair_evaluator_code_provenance import FAIREvaluatorCodeProvenance
from fuji_server.evaluators.fair_evaluator_community_metadata import FAIREvaluatorCommunityMetadata
from fuji_server.evaluators.fair_evaluator_data_access_level import FAIREvaluatorDataAccessLevel
from fuji_server.evaluators.fair_evaluator_data_content_metadata import FAIREvaluatorDataContentMetadata
from fuji_server.evaluators.fair_evaluator_data_identifier_included import FAIREvaluatorDataIdentifierIncluded
from fuji_server.evaluators.fair_evaluator_data_provenance import FAIREvaluatorDataProvenance
from fuji_server.evaluators.fair_evaluator_development_metadata import FAIREvaluatorDevelopmentMetadata
from fuji_server.evaluators.fair_evaluator_file_format import FAIREvaluatorFileFormat
from fuji_server.evaluators.fair_evaluator_formal_metadata import FAIREvaluatorFormalMetadata
from fuji_server.evaluators.fair_evaluator_license import FAIREvaluatorLicense
from fuji_server.evaluators.fair_evaluator_license_file import FAIREvaluatorLicenseFile
from fuji_server.evaluators.fair_evaluator_metadata_identifier_included import FAIREvaluatorMetadataIdentifierIncluded
from fuji_server.evaluators.fair_evaluator_metadata_preservation import FAIREvaluatorMetadataPreserved
from fuji_server.evaluators.fair_evaluator_minimal_metadata import FAIREvaluatorCoreMetadata
from fuji_server.evaluators.fair_evaluator_persistent_identifier_data import FAIREvaluatorPersistentIdentifierData
from fuji_server.evaluators.fair_evaluator_persistent_identifier_metadata import (
FAIREvaluatorPersistentIdentifierMetadata,
)
from fuji_server.evaluators.fair_evaluator_related_resources import FAIREvaluatorRelatedResources
from fuji_server.evaluators.fair_evaluator_requirements import FAIREvaluatorRequirements
from fuji_server.evaluators.fair_evaluator_searchable import FAIREvaluatorSearchable
from fuji_server.evaluators.fair_evaluator_semantic_vocabulary import FAIREvaluatorSemanticVocabulary
from fuji_server.evaluators.fair_evaluator_software_component_identifier import FAIREvaluatorSoftwareComponentIdentifier
from fuji_server.evaluators.fair_evaluator_standardised_protocol_data import FAIREvaluatorStandardisedProtocolData
from fuji_server.evaluators.fair_evaluator_standardised_protocol_metadata import (
FAIREvaluatorStandardisedProtocolMetadata,
)
from fuji_server.evaluators.fair_evaluator_test_cases import FAIREvaluatorTestCases
from fuji_server.evaluators.fair_evaluator_unique_identifier_data import FAIREvaluatorUniqueIdentifierData
from fuji_server.evaluators.fair_evaluator_unique_identifier_metadata import FAIREvaluatorUniqueIdentifierMetadata
from fuji_server.evaluators.fair_evaluator_unique_persistent_identifier_software import (
FAIREvaluatorUniquePersistentIdentifierSoftware,
)
from fuji_server.evaluators.fair_evaluator_version_identifier import FAIREvaluatorVersionIdentifier
from fuji_server.harvester.data_harvester import DataHarvester
from fuji_server.harvester.github_harvester import GithubHarvester
from fuji_server.harvester.metadata_harvester import MetadataHarvester
from fuji_server.helper.linkedvocabhelper import LinkedVocabHelper
from fuji_server.helper.metadata_collector import MetadataOfferingMethods
from fuji_server.helper.metadata_mapper import Mapper
from fuji_server.helper.metric_helper import MetricHelper
from fuji_server.helper.preprocessor import Preprocessor
from fuji_server.helper.repository_helper import RepositoryHelper
class FAIRCheck:
METRICS = None
METRIC_VERSION = None
SPDX_LICENSES = None
SPDX_LICENSE_NAMES = None
"""COMMUNITY_METADATA_STANDARDS_NAMES = None
COMMUNITY_METADATA_STANDARDS_URIS = None
COMMUNITY_METADATA_STANDARDS = None"""
SCIENCE_FILE_FORMATS = None
LONG_TERM_FILE_FORMATS = None
OPEN_FILE_FORMATS = None
DEFAULT_NAMESPACES = None
VOCAB_NAMESPACES = None
ARCHIVE_MIMETYPES = Mapper.ARCHIVE_COMPRESS_MIMETYPES.value
STANDARD_PROTOCOLS = None
SCHEMA_ORG_CONTEXT = []
FILES_LIMIT = None
LOG_SUCCESS = 25
LOG_FAILURE = 35
VALID_RESOURCE_TYPES = []
IDENTIFIERS_ORG_DATA = {}
GOOGLE_DATA_DOI_CACHE = []
GOOGLE_DATA_URL_CACHE = []
LINKED_VOCAB_INDEX = {}
ACCESS_RIGHTS = {}
FUJI_VERSION = __version__
def __init__(
self,
uid,
test_debug=False,
metadata_service_url=None,
metadata_service_type=None,
use_datacite=True,
use_github=False,
verify_pids=True,
oaipmh_endpoint=None,
metric_version=None,
): # e.g. metrics_v0.5 regex: metrics_v([0-9]+\.[0-9]+)(_[a-z]+)?
uid_bytes = uid.encode("utf-8")
self.test_id = hashlib.sha1(uid_bytes).hexdigest()
# str(base64.urlsafe_b64encode(uid_bytes), "utf-8") # an id we can use for caching etc
if isinstance(uid, str):
uid = uid.strip()
self.id = self.input_id = uid
self.metadata_service_url = metadata_service_url
self.metadata_service_type = metadata_service_type
self.oaipmh_endpoint = oaipmh_endpoint
self.csw_endpoint = None
self.sparql_endpoint = None
if self.oaipmh_endpoint:
self.metadata_service_url = self.oaipmh_endpoint
self.metadata_service_type = "oai_pmh"
if self.metadata_service_type == "oai_pmh":
self.oaipmh_endpoint = self.metadata_service_url
elif str(self.metadata_service_type) == "ogc_csw" or "csw" in str(self.metadata_service_type):
self.csw_endpoint = self.metadata_service_url
elif self.metadata_service_type == "sparql":
self.sparql_endpoint = self.metadata_service_url
self.pid_url = None # full pid # e.g., "https://doi.org/10.1594/pangaea.906092 or url (non-pid)
self.landing_url = None # url of the landing page of self.pid_url
self.origin_url = None # the url from where all starts - in case of redirection we'll need this later on
self.repository_urls = [] # urls identified which could represent the repository will need this probably for FAIRiCAT things
self.landing_html = None
self.landing_content_type = None
self.landing_origin = None # schema + authority of the landing page e.g. https://www.pangaea.de
self.signposting_header_links = []
self.typed_links = []
self.pid_scheme = None
self.id_scheme = None
self.checked_pages = []
self.logger = logging.getLogger(self.test_id)
self.metadata_sources = []
self.isDebug = test_debug
self.isLandingPageAccessible = None
self.metadata_merged = {}
self.metadata_unmerged = []
self.content_identifier = {}
self.community_standards = []
self.community_standards_uri = {}
self.namespace_uri = []
self.linked_namespace_uri = {}
self.reference_elements = (
Mapper.REFERENCE_METADATA_LIST.value.copy()
) # all metadata elements required for FUJI metrics
self.related_resources = []
# self.test_data_content_text = None# a helper to check metadata against content
self.rdf_graph = None
self.rdf_collector = None
self.use_datacite = use_datacite
self.use_github = use_github
self.repeat_pid_check = False
self.logger_message_stream = io.StringIO()
logging.addLevelName(self.LOG_SUCCESS, "SUCCESS")
logging.addLevelName(self.LOG_FAILURE, "FAILURE")
# in case log messages shall be sent to a remote server
self.remoteLogPath = None
self.remoteLogHost = None
self.weblogger = None
if self.isDebug:
self.logStreamHandler = logging.StreamHandler(self.logger_message_stream)
formatter = logging.Formatter("%(message)s|%(levelname)s")
self.logStreamHandler.setFormatter(formatter)
self.logger.propagate = False
self.logger.setLevel(logging.INFO) # set to debug in testing environment
self.logger.addHandler(self.logStreamHandler)
if Preprocessor.remote_log_host:
self.weblogger = logging.handlers.HTTPHandler(
Preprocessor.remote_log_host,
Preprocessor.remote_log_path + "?testid=" + str(self.test_id),
method="POST",
)
self.webformatter = logging.Formatter("%(levelname)s - %(message)s \r\n")
self.verify_pids = Preprocessor.verify_pids
if not self.verify_pids:
self.logger.warning(
"FsF-F1-02D : Verification of PIDs is disabled in the config file, the evaluation result may be misleading"
)
self.count = 0
FAIRCheck.load_predata()
# self.extruct = None
self.extruct_result = {}
self.lov_helper = LinkedVocabHelper(self.LINKED_VOCAB_INDEX)
self.auth_token = None
self.auth_token_type = "Basic"
self.pid_collector = {}
if not metric_version:
metric_version = "metrics_v0.5"
self.logger.warning("FsF-F1-02 : Metrics version not given, therefore loading default metrics v0.5")
self.metric_helper = MetricHelper(metric_version)
self.METRICS = self.metric_helper.get_custom_metrics(
["metric_name", "total_score", "metric_tests", "metric_number"]
)
self.METRIC_VERSION = metric_version
self.metrics_config = self.metric_helper.get_metrics_config()
print("METRICS CONFIG: ", self.metrics_config)
allowed_harvesting_methods = self.metrics_config.get("allowed_harvesting_methods")
allowed_metadata_standards = self.metrics_config.get("allowed_metadata_standards")
if not isinstance(allowed_metadata_standards, list):
allowed_metadata_standards = None
else:
print("ALLOWED METADATA STANDARDS: ", allowed_metadata_standards)
if allowed_harvesting_methods:
print("ALLOWED METADATA OFFERING METHODS: ", allowed_harvesting_methods)
if not isinstance(allowed_harvesting_methods, list):
allowed_harvesting_methods = None
else:
allowed_harvesting_methods = [
MetadataOfferingMethods[m]
for m in allowed_harvesting_methods
if m in MetadataOfferingMethods._member_names_
]
self.metadata_harvester = MetadataHarvester(
self.id,
use_datacite=use_datacite,
logger=self.logger,
allowed_harvesting_methods=allowed_harvesting_methods,
allowed_metadata_standards=allowed_metadata_standards,
)
self.repo_helper = None
@classmethod
def load_predata(cls):
cls.FILES_LIMIT = Preprocessor.data_files_limit
if not cls.SPDX_LICENSES:
cls.SPDX_LICENSES, cls.SPDX_LICENSE_NAMES = Preprocessor.get_licenses()
"""if not cls.COMMUNITY_METADATA_STANDARDS:
cls.COMMUNITY_METADATA_STANDARDS = Preprocessor.get_metadata_standards()
cls.COMMUNITY_METADATA_STANDARDS_URIS = {u.strip().strip('#/') : k for k, v in cls.COMMUNITY_METADATA_STANDARDS.items() for u in v.get('urls')}
cls.COMMUNITY_METADATA_STANDARDS_NAMES = {k: v.get('title') for k,v in cls.COMMUNITY_METADATA_STANDARDS.items()}"""
if not cls.SCIENCE_FILE_FORMATS:
cls.SCIENCE_FILE_FORMATS = Preprocessor.get_science_file_formats()
if not cls.LONG_TERM_FILE_FORMATS:
cls.LONG_TERM_FILE_FORMATS = Preprocessor.get_long_term_file_formats()
if not cls.OPEN_FILE_FORMATS:
cls.OPEN_FILE_FORMATS = Preprocessor.get_open_file_formats()
if not cls.DEFAULT_NAMESPACES:
cls.DEFAULT_NAMESPACES = Preprocessor.getDefaultNamespaces()
if not cls.VOCAB_NAMESPACES:
cls.VOCAB_NAMESPACES = Preprocessor.getLinkedVocabs()
if not cls.STANDARD_PROTOCOLS:
cls.STANDARD_PROTOCOLS = Preprocessor.get_standard_protocols()
if not cls.SCHEMA_ORG_CONTEXT:
cls.SCHEMA_ORG_CONTEXT = Preprocessor.get_schema_org_context()
if not cls.VALID_RESOURCE_TYPES:
cls.VALID_RESOURCE_TYPES = Preprocessor.get_resource_types()
if not cls.IDENTIFIERS_ORG_DATA:
cls.IDENTIFIERS_ORG_DATA = Preprocessor.get_identifiers_org_data()
if not cls.LINKED_VOCAB_INDEX:
cls.LINKED_VOCAB_INDEX = Preprocessor.get_linked_vocab_index()
if not cls.ACCESS_RIGHTS:
cls.ACCESS_RIGHTS = Preprocessor.get_access_rights()
# TODO: change this
# Preprocessor.set_mime_types()
# not needed locally ... but init class variable
# Preprocessor.get_google_data_dois()
# Preprocessor.get_google_data_urls()
@staticmethod
def uri_validator(u): # TODO integrate into request_helper.py
try:
r = urlparse(u)
return all([r.scheme, r.netloc])
except:
return False
def set_auth_token(self, auth_token, auth_token_type="Basic"):
if auth_token:
self.auth_token = auth_token
self.metadata_harvester.auth_token = self.auth_token
if auth_token_type:
if auth_token_type in ["Basic", "Bearer"]:
self.auth_token_type = auth_token_type
self.metadata_harvester.auth_token_type = self.auth_token_type
else:
self.auth_token_type = "Basic"
def clean_metadata(self):
# replace nasty "None" strings by real None
try:
nonerepdict = json.dumps(self.metadata_merged).replace('"None"', "null")
self.metadata_merged = json.loads(nonerepdict)
except:
print("Nasty None replace error")
pass
data_objects = self.metadata_merged.get("object_content_identifier")
if data_objects == {"url": None} or data_objects == [None]:
data_objects = self.metadata_merged["object_content_identifier"] = None
if data_objects is not None:
if not isinstance(data_objects, list):
self.metadata_merged["object_content_identifier"] = [data_objects]
# duplicate handling
if self.metadata_merged.get("object_content_identifier"):
fdci = {}
for dci in self.metadata_merged.get("object_content_identifier"):
dcurl = dci.get("url")
if dcurl not in fdci:
fdci[dcurl] = dci
else:
# complete size and type
if not fdci[dcurl].get("type") and dci.get("type"):
fdci[dcurl]["type"] = dci.get("type")
if not fdci[dcurl].get("size") and dci.get("size"):
fdci[dcurl]["size"] = dci.get("size")
self.metadata_merged["object_content_identifier"] = [di for di in fdci.values()]
# if "object_content_identifier" in self.metadata_merged:
# if self.metadata_merged.get("object_content_identifier"):
oi = 0
for c in self.metadata_merged["object_content_identifier"]:
if (
not c.get("size")
and self.metadata_merged.get("object_size")
and len(self.metadata_merged["object_content_identifier"]) == 1
):
# c["size"] = self.metadata_merged.get("object_size")
self.metadata_merged["object_content_identifier"][oi]["size"] = self.metadata_merged.get(
"object_size"
)
# clean mime types in case these are in URI form:
if c.get("type"):
if isinstance(c["type"], list):
c["type"] = c["type"][0]
self.metadata_merged["object_content_identifier"][oi]["type"] = c["type"][0]
mime_parts = str(c.get("type")).split("/")
if len(mime_parts) > 2:
if mime_parts[-2] in [
"application",
"audio",
"font",
"example",
"image",
"message",
"model",
"multipart",
"text",
"video",
]:
self.metadata_merged["object_content_identifier"][oi]["type"] = (
str(mime_parts[-2]) + "/" + str(mime_parts[-1])
)
oi += 1
# clean empty entries
for mk, mv in list(self.metadata_merged.items()):
if mv == "" or mv is None:
del self.metadata_merged[mk]
def harvest_all_metadata(self):
# ========= clean merged metadata, delete all entries which are None or ''
self.retrieve_metadata_embedded()
self.retrieve_metadata_external()
self.logger.info(
"FsF-F2-01M : Type of object described by the metadata -: {}".format(
self.metadata_merged.get("object_type")
)
)
# detect api and standards
# self.retrieve_apis_standards()
# remove duplicates
if self.namespace_uri:
self.namespace_uri = list(set(self.namespace_uri))
def harvest_re3_data(self):
if self.use_datacite:
client_id = self.metadata_merged.get("datacite_client")
self.logger.info(f"FsF-R1.3-01M : re3data/datacite client id -: {client_id}")
self.repo_helper = RepositoryHelper(client_id=client_id, logger=self.logger, landingpage=self.landing_url)
self.repo_helper.lookup_re3data()
else:
self.client_id = None
self.logger.warning(
"{} : Datacite support disabled, therefore skipping standards identification using in re3data record".format(
"FsF-R1.3-01M",
)
)
def harvest_all_data(self):
if self.metadata_merged.get("object_content_identifier"):
data_links = self.metadata_merged.get("object_content_identifier") # [: self.FILES_LIMIT]
data_harvester = DataHarvester(data_links, self.logger, self.landing_url, metrics=self.METRICS.keys())
data_harvester.retrieve_all_data()
self.content_identifier = data_harvester.data
def harvest_github(self):
if self.use_github:
github_harvester = GithubHarvester(self.id, self.logger)
github_harvester.harvest()
self.github_data = github_harvester.data
else:
self.github_data = {}
# NOTE: Update list of metrics that are impacted by this as more are implemented.
for m in ["FRSM-15-R1.1"]:
self.logger.warning(f"{m} : Github support disabled, therefore skipping harvesting through Github API")
def retrieve_metadata_embedded(self):
self.metadata_harvester.retrieve_metadata_embedded()
# self.metadata_unmerged.extend(self.metadata_harvester.metadata_unmerged)
# self.metadata_merged.update(self.metadata_harvester.metadata_merged)
self.repeat_pid_check = self.metadata_harvester.repeat_pid_check
self.namespace_uri.extend(self.metadata_harvester.namespace_uri)
self.metadata_sources.extend(self.metadata_harvester.metadata_sources)
self.linked_namespace_uri.update(self.metadata_harvester.linked_namespace_uri)
self.related_resources.extend(self.metadata_harvester.related_resources)
self.landing_url = self.metadata_harvester.landing_url
self.landing_origin = self.metadata_harvester.landing_origin
self.landing_domain = self.metadata_harvester.landing_domain
self.origin_url = self.metadata_harvester.origin_url
self.pid_url = self.metadata_harvester.pid_url
self.pid_scheme = self.metadata_harvester.pid_scheme
self.pid_collector.update(self.metadata_harvester.pid_collector)
def retrieve_metadata_external(self, target_url=None, repeat_mode=False):
self.metadata_harvester.retrieve_metadata_external(target_url, repeat_mode=repeat_mode)
# self.metadata_unmerged.extend(self.metadata_harvester.metadata_unmerged)
# self.metadata_merged.update(self.metadata_harvester.metadata_merged)
self.repeat_pid_check = self.metadata_harvester.repeat_pid_check
self.namespace_uri.extend(self.metadata_harvester.namespace_uri)
self.metadata_sources.extend(self.metadata_harvester.metadata_sources)
self.linked_namespace_uri.update(self.metadata_harvester.linked_namespace_uri)
self.related_resources.extend(self.metadata_harvester.related_resources)
self.metadata_harvester.get_signposting_object_identifier()
self.pid_url = self.metadata_harvester.pid_url
self.pid_scheme = self.metadata_harvester.pid_scheme
self.pid_collector.update(self.metadata_harvester.pid_collector)
def set_harvested_metadata(self):
self.metadata_unmerged = self.metadata_harvester.metadata_unmerged
self.metadata_merged = self.metadata_harvester.metadata_merged
self.clean_metadata()
def check_unique_metadata_identifier(self):
unique_identifier_check = FAIREvaluatorUniqueIdentifierMetadata(self)
return unique_identifier_check.getResult()
def check_unique_content_identifier(self):
unique_identifier_check = FAIREvaluatorUniqueIdentifierData(self)
return unique_identifier_check.getResult()
def check_persistent_metadata_identifier(self):
persistent_identifier_check = FAIREvaluatorPersistentIdentifierMetadata(self)
return persistent_identifier_check.getResult()
def check_persistent_data_identifier(self):
persistent_identifier_check = FAIREvaluatorPersistentIdentifierData(self)
return persistent_identifier_check.getResult()
def check_unique_persistent_metadata_identifier(self):
return self.check_unique_metadata_identifier(), self.check_persistent_metadata_identifier()
def check_unique_persistent_software_identifier(self):
unique_persistent_identifier_check = FAIREvaluatorUniquePersistentIdentifierSoftware(self)
return unique_persistent_identifier_check.getResult()
def check_software_component_identifier(self):
component_identifier_check = FAIREvaluatorSoftwareComponentIdentifier(self)
return component_identifier_check.getResult()
def check_version_identifier(self):
version_identifier_check = FAIREvaluatorVersionIdentifier(self)
return version_identifier_check.getResult()
def check_development_metadata(self):
development_metadata_check = FAIREvaluatorDevelopmentMetadata(self)
return development_metadata_check.getResult()
def check_open_api(self):
open_api_check = FAIREvaluatorAPI(self)
return open_api_check.getResult()
def check_requirements(self):
requirements_check = FAIREvaluatorRequirements(self)
return requirements_check.getResult()
def check_test_cases(self):
test_cases_check = FAIREvaluatorTestCases(self)
return test_cases_check.getResult()
def check_minimal_metatadata(self, include_embedded=True):
core_metadata_check = FAIREvaluatorCoreMetadata(self)
return core_metadata_check.getResult()
def check_data_identifier_included_in_metadata(self):
data_identifier_included_check = FAIREvaluatorDataIdentifierIncluded(self)
return data_identifier_included_check.getResult()
def check_metadata_identifier_included_in_metadata(self):
metadata_identifier_included_check = FAIREvaluatorMetadataIdentifierIncluded(self)
return metadata_identifier_included_check.getResult()
def check_data_access_level(self):
data_access_level_check = FAIREvaluatorDataAccessLevel(self)
return data_access_level_check.getResult()
def check_license(self):
license_check = FAIREvaluatorLicense(self)
return license_check.getResult()
def check_license_file(self):
license_check = FAIREvaluatorLicenseFile(self)
return license_check.getResult()
def check_relatedresources(self):
related_check = FAIREvaluatorRelatedResources(self)
return related_check.getResult()
def check_searchable(self):
searchable_check = FAIREvaluatorSearchable(self)
return searchable_check.getResult()
def check_data_file_format(self):
data_file_check = FAIREvaluatorFileFormat(self)
return data_file_check.getResult()
def check_community_metadatastandards(self):
community_metadata_check = FAIREvaluatorCommunityMetadata(self)
return community_metadata_check.getResult()
def check_data_provenance(self):
data_prov_check = FAIREvaluatorDataProvenance(self)
return data_prov_check.getResult()
def check_code_provenance(self):
code_prov_check = FAIREvaluatorCodeProvenance(self)
return code_prov_check.getResult()
def check_data_content_metadata(self):
data_content_metadata_check = FAIREvaluatorDataContentMetadata(self)
return data_content_metadata_check.getResult()
def check_formal_metadata(self):
formal_metadata_check = FAIREvaluatorFormalMetadata(self)
return formal_metadata_check.getResult()
def check_semantic_vocabulary(self):
semantic_vocabulary_check = FAIREvaluatorSemanticVocabulary(self)
return semantic_vocabulary_check.getResult()
def check_metadata_preservation(self):
metadata_preserved_check = FAIREvaluatorMetadataPreserved(self)
return metadata_preserved_check.getResult()
def check_standardised_protocol_data(self):
standardised_protocol_check = FAIREvaluatorStandardisedProtocolData(self)
return standardised_protocol_check.getResult()
def check_standardised_protocol_metadata(self):
standardised_protocol_metadata_check = FAIREvaluatorStandardisedProtocolMetadata(self)
return standardised_protocol_metadata_check.getResult()
"""def raise_warning_if_javascript_page(self, response_content):
# check if javascript generated content only:
try:
soup = BeautifulSoup(response_content, features="html.parser")
script_content = soup.findAll("script")
for script in soup(["script", "style", "title", "noscript"]):
script.extract()
text_content = soup.get_text(strip=True)
if (len(str(script_content)) > len(str(text_content))) and len(text_content) <= 150:
self.logger.warning(
"FsF-F1-02D : Landing page seems to be JavaScript generated, could not detect enough content"
)
except Exception:
pass
"""
def get_log_messages_dict(self):
logger_messages = {}
self.logger_message_stream.seek(0)
for log_message in self.logger_message_stream.readlines():
if log_message.startswith("FsF-") or log_message.startswith("FRSM-"):
m = log_message.split(":", 1)
metric = m[0].strip()
message_n_level = m[1].strip().split("|", 1)
if len(message_n_level) > 1:
level = message_n_level[1]
else:
level = "INFO"
message = message_n_level[0]
if metric not in logger_messages:
logger_messages[metric] = []
if message not in logger_messages[metric]:
logger_messages[metric].append(level.replace("\n", "") + ": " + message.strip())
self.logger_message_stream = io.StringIO
return logger_messages
def get_assessment_summary(self, results):
status_dict = {"pass": 1, "fail": 0}
summary_dict = {
"fair_category": [],
"fair_principle": [],
"score_earned": [],
"score_total": [],
"maturity": [],
"status": [],
}
for res_k, res_v in enumerate(results):
if res_v.get("metric_identifier"):
metric_match = re.search(
r"^(?:FRSM-[0-9]+|FsF)-(([FAIR])[0-9](\.[0-9])?)", str(res_v.get("metric_identifier"))
) # match both FAIR and FsF metrics
if metric_match.group(2) is not None:
fair_principle = metric_match[1]
fair_category = metric_match[2]
earned_maturity = res_v["maturity"]
# earned_maturity = [k for k, v in maturity_dict.items() if v == res_v['maturity']][0]
summary_dict["fair_category"].append(fair_category)
summary_dict["fair_principle"].append(fair_principle)
# An easter egg for Mustapha
if self.input_id in [
"https://www.rd-alliance.org/users/mustapha-mokrane",
"https://www.rd-alliance.org/users/ilona-von-stein",
]:
summary_dict["score_earned"].append(res_v["score"]["total"])
summary_dict["maturity"].append(3)
summary_dict["status"].append(1)
else:
summary_dict["score_earned"].append(res_v["score"]["earned"])
summary_dict["maturity"].append(earned_maturity)
summary_dict["status"].append(status_dict.get(res_v["test_status"]))
summary_dict["score_total"].append(res_v["score"]["total"])
sf = pd.DataFrame(summary_dict)
summary = {"score_earned": {}, "score_total": {}, "score_percent": {}, "status_total": {}, "status_passed": {}}
summary["score_earned"] = sf.groupby(by="fair_category")["score_earned"].sum().to_dict()
summary["score_earned"].update(sf.groupby(by="fair_principle")["score_earned"].sum().to_dict())
summary["score_earned"]["FAIR"] = round(float(sf["score_earned"].sum()), 2)
summary["score_total"] = sf.groupby(by="fair_category")["score_total"].sum().to_dict()
summary["score_total"].update(sf.groupby(by="fair_principle")["score_total"].sum().to_dict())
summary["score_total"]["FAIR"] = round(float(sf["score_total"].sum()), 2)
summary["score_percent"] = (
round(
sf.groupby(by="fair_category")["score_earned"].sum()
/ sf.groupby(by="fair_category")["score_total"].sum()
* 100,
2,
)
).to_dict()
summary["score_percent"].update(
(
round(
sf.groupby(by="fair_principle")["score_earned"].sum()
/ sf.groupby(by="fair_principle")["score_total"].sum()
* 100,
2,
)
).to_dict()
)
summary["score_percent"]["FAIR"] = round(float(sf["score_earned"].sum() / sf["score_total"].sum() * 100), 2)
summary["maturity"] = (
sf.groupby(by="fair_category")["maturity"]
.apply(lambda x: 1 if x.mean() < 1 and x.mean() > 0 else round(x.mean()))
.to_dict()
)
summary["maturity"].update(
sf.groupby(by="fair_principle")["maturity"]
.apply(lambda x: 1 if x.mean() < 1 and x.mean() > 0 else round(x.mean()))
.to_dict()
)
total_maturity = 0
for fair_index in ["F", "A", "I", "R"]:
if summary["maturity"].get(fair_index):
total_maturity += summary["maturity"][fair_index]
summary["maturity"]["FAIR"] = round(
float(1 if total_maturity / 4 < 1 and total_maturity / 4 > 0 else total_maturity / 4), 2
)
summary["status_total"] = sf.groupby(by="fair_principle")["status"].count().to_dict()
summary["status_total"].update(sf.groupby(by="fair_category")["status"].count().to_dict())
summary["status_total"]["FAIR"] = int(sf["status"].count())
summary["status_passed"] = sf.groupby(by="fair_principle")["status"].sum().to_dict()
summary["status_passed"].update(sf.groupby(by="fair_category")["status"].sum().to_dict())
summary["status_passed"]["FAIR"] = int(sf["status"].sum())
return summary
def set_repository_uris(self):
if self.landing_origin:
self.repository_urls.append(self.landing_origin)
if self.metadata_merged.get("publisher"):
if not isinstance(self.metadata_merged.get("publisher"), list):
self.metadata_merged["publisher"] = [self.metadata_merged.get("publisher")]
for publisher_url in self.metadata_merged.get("publisher"):
if self.uri_validator(publisher_url):
if self.landing_domain in publisher_url and publisher_url.count("/") <= 3:
self.repository_urls.append(publisher_url)
if self.repository_urls:
self.repository_urls = list(set(self.repository_urls))
print("REPOSITORY URIS: ", self.repository_urls)
def set_repository_info(self):
self.set_repository_uris()
if self.repository_urls:
for repo_uri in self.repository_urls:
repoharvester = MetadataHarvester(repo_uri)
repoharvester.retrieve_metadata_embedded()
repoharvester.retrieve_metadata_external()
print("########################### REPO METADATA")
print(repoharvester.metadata_merged)