Skip to content

Commit

Permalink
Creating EvaluatorBase
Browse files Browse the repository at this point in the history
  • Loading branch information
@ferag
ferag committed Oct 16, 2024
1 parent 670375b commit 7ddf874
Show file tree
Hide file tree
Showing 3 changed files with 108 additions and 224 deletions.
266 changes: 72 additions & 194 deletions api/evaluator.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import sys
import urllib
import xml.etree.ElementTree as ET
from abc import ABC, abstractmethod
from functools import wraps

import idutils
Expand Down Expand Up @@ -63,53 +64,7 @@ def wrapper(plugin, **kwargs):
return wrapper


class ConfigTerms(property):
def __init__(self, term_id):
self.term_id = term_id

def __call__(self, wrapped_func):
@wraps(wrapped_func)
def wrapper(plugin, **kwargs):
metadata = plugin.metadata
has_metadata = True

term_list = ast.literal_eval(plugin.config[plugin.name][self.term_id])
# Get values in config for the given term
if not term_list:
msg = (
"Cannot find any value for term <%s> in configuration"
% self.term_id
)
has_metadata = False
else:
# Get metadata associated with the term ID
term_metadata = pd.DataFrame(
term_list, columns=["element", "qualifier"]
)
term_metadata = ut.check_metadata_terms_with_values(
metadata, term_metadata
)
if term_metadata.empty:
msg = (
"No access information can be found in the metadata for: %s. Please double-check the value/s provided for '%s' configuration parameter"
% (term_list, self.term_id)
)
has_metadata = False

if not has_metadata:
logger.warning(msg)
return (0, [{"message": msg, "points": 0}])

# Update kwargs with collected metadata for the required terms
kwargs.update(
{self.term_id: {"list": term_list, "metadata": term_metadata}}
)
return wrapped_func(plugin, **kwargs)

return wrapper


class Evaluator(object):
class EvaluatorBase(ABC):
"""A class used to define FAIR indicators tests. It contains all the references to all the tests
...
Expand All @@ -126,115 +81,79 @@ class Evaluator(object):
lang : Language
"""

def __init__(self, item_id, oai_base=None, lang="en", plugin=None, config=None):
def __init__(self, item_id, oai_base=None, lang="en", config=None, name=None):
self.item_id = item_id
self.oai_base = oai_base
self.metadata = None
self.access_protocols = []
self.cvs = []
self.config = config
# configuration terms
self.terms_access_metadata = pd.DataFrame()
self.terms_license_metadata = pd.DataFrame()

logger.debug("OAI_BASE IN evaluator: %s" % oai_base)
if oai_base is not None and oai_base != "" and self.metadata is None:
metadataFormats = ut.oai_metadataFormats(oai_base)
dc_prefix = ""
for e in metadataFormats:
if metadataFormats[e] == "http://www.openarchives.org/OAI/2.0/oai_dc/":
dc_prefix = e
logger.debug("DC_PREFIX: %s" % dc_prefix)

try:
id_type = idutils.detect_identifier_schemes(self.item_id)[0]
except Exception as e:
id_type = "internal"

logger.debug("Trying to get metadata")
try:
item_metadata = ut.oai_get_metadata(
ut.oai_check_record_url(oai_base, dc_prefix, self.item_id)
).find(".//{http://www.openarchives.org/OAI/2.0/}metadata")
except Exception as e:
logger.error("Problem getting metadata: %s" % e)
item_metadata = ET.fromstring("<metadata></metadata>")
data = []
for tags in item_metadata.findall(".//"):
metadata_schema = tags.tag[0 : tags.tag.rfind("}") + 1]
element = tags.tag[tags.tag.rfind("}") + 1 : len(tags.tag)]
text_value = tags.text
qualifier = None
data.append([metadata_schema, element, text_value, qualifier])
self.metadata = pd.DataFrame(
data, columns=["metadata_schema", "element", "text_value", "qualifier"]
)

if self.metadata is not None:
if len(self.metadata) > 0:
self.access_protocols = ["http", "oai-pmh"]

# Config attributes
self.name = plugin
if self.name == None:
self.name = "oai-pmh"
try:
self.identifier_term = ast.literal_eval(
self.config[self.name]["identifier_term"]
)
self.terms_quali_generic = ast.literal_eval(
self.config[self.name]["terms_quali_generic"]
)
self.terms_quali_disciplinar = ast.literal_eval(
self.config[self.name]["terms_quali_disciplinar"]
)
self.terms_access = ast.literal_eval(self.config[self.name]["terms_access"])
self.terms_cv = ast.literal_eval(self.config[self.name]["terms_cv"])
self.supported_data_formats = ast.literal_eval(
self.config[self.name]["supported_data_formats"]
)
self.terms_qualified_references = ast.literal_eval(
self.config[self.name]["terms_qualified_references"]
)
self.terms_relations = ast.literal_eval(
self.config[self.name]["terms_relations"]
)
self.terms_license = ast.literal_eval(
self.config[self.name]["terms_license"]
)
self.metadata_quality = 100 # Value for metadata quality
self.terms_access_protocols = ast.literal_eval(
self.config[self.name]["terms_access_protocols"]
)
self.metadata_standard = ast.literal_eval(
self.config[self.name]["metadata_standard"]
)
self.fairsharing_username = ast.literal_eval(
self.config["fairsharing"]["username"]
)
self.identifier_term = ast.literal_eval(
self.config[self.name]["identifier_term"]
)
self.terms_quali_generic = ast.literal_eval(
self.config[self.name]["terms_quali_generic"]
)
self.terms_quali_disciplinar = ast.literal_eval(
self.config[self.name]["terms_quali_disciplinar"]
)
self.terms_cv = ast.literal_eval(self.config[self.name]["terms_cv"])
self.supported_data_formats = ast.literal_eval(
self.config[self.name]["supported_data_formats"]
)
self.terms_qualified_references = ast.literal_eval(
self.config[self.name]["terms_qualified_references"]
)
self.terms_relations = ast.literal_eval(
self.config[self.name]["terms_relations"]
)
self.metadata_access_manual = ast.literal_eval(
self.config[self.name]["metadata_access_manual"]
)
self.data_access_manual = ast.literal_eval(
self.config[self.name]["data_access_manual"]
)
self.terms_access_protocols = ast.literal_eval(
self.config[self.name]["terms_access_protocols"]
)

self.fairsharing_password = ast.literal_eval(
self.config["fairsharing"]["password"]
)
self.fairsharing_metadata_path = ast.literal_eval(
self.config["fairsharing"]["metadata_path"]
)
self.fairsharing_formats_path = ast.literal_eval(
self.config["fairsharing"]["formats_path"]
)
self.internet_media_types_path = ast.literal_eval(
self.config["internet media types"]["path"]
)
self.metadata_schemas = ast.literal_eval(
self.config[self.name]["metadata_schemas"]
)
except Exception as e:
logger.error("Problem loading plugin config: %s" % e)
# self.vocabularies = ast.literal_eval(self.config[self.name]["vocabularies"])

# Translations
self.lang = lang
logger.debug("El idioma es: %s" % self.lang)
logger.debug("METAdata: %s" % self.metadata)
self.dict_vocabularies = ast.literal_eval(
self.config[self.name]["dict_vocabularies"]
)

self.vocabularies = list(self.dict_vocabularies.keys())
self.metadata_standard = ast.literal_eval(
self.config[self.name]["metadata_standard"]
)

self.metadata_authentication = ast.literal_eval(
self.config[self.name]["metadata_authentication"]
)
self.metadata_persistence = ast.literal_eval(
self.config[self.name]["metadata_persistence"]
)
self.terms_vocabularies = ast.literal_eval(
self.config[self.name]["terms_vocabularies"]
)

self.fairsharing_username = ast.literal_eval(
self.config["fairsharing"]["username"]
)

self.fairsharing_password = ast.literal_eval(
self.config["fairsharing"]["password"]
)
self.fairsharing_metadata_path = ast.literal_eval(
self.config["fairsharing"]["metadata_path"]
)
self.fairsharing_formats_path = ast.literal_eval(
self.config["fairsharing"]["formats_path"]
)
self.internet_media_types_path = ast.literal_eval(
self.config["internet media types"]["path"]
)
global _
_ = self.translation()

Expand Down Expand Up @@ -267,6 +186,11 @@ def eval_persistency(self, id_list, data_or_metadata="(meta)data"):

return (points, msg_list)

@abstractmethod
def get_metadata(self):
"""Method to be implemented by plugins."""
raise NotImplementedError("Derived class mus implement get_metadata method")

def eval_uniqueness(self, id_list, data_or_metadata="(meta)data"):
points = 0
msg_list = []
Expand Down Expand Up @@ -2066,49 +1990,3 @@ def check_standard_license(self, license_id_or_url):
% _url
)
return license_name


class ConfigTerms(property):
def __init__(self, term_id):
self.term_id = term_id

def __call__(self, wrapped_func):
@wraps(wrapped_func)
def wrapper(plugin, **kwargs):
metadata = plugin.metadata
has_metadata = True

term_list = ast.literal_eval(plugin.config[plugin.name][self.term_id])
# Get values in config for the given term
if not term_list:
msg = (
"Cannot find any value for term <%s> in configuration"
% self.term_id
)
has_metadata = False
else:
# Get metadata associated with the term ID
term_metadata = pd.DataFrame(
term_list, columns=["element", "qualifier"]
)
term_metadata = ut.check_metadata_terms_with_values(
metadata, term_metadata
)
if term_metadata.empty:
msg = (
"No access information can be found in the metadata for: %s. Please double-check the value/s provided for '%s' configuration parameter"
% (term_list, self.term_id)
)
has_metadata = False

if not has_metadata:
logger.warning(msg)
return (0, msg)

# Update kwargs with collected metadata for the required terms
kwargs.update(
{self.term_id: {"list": term_list, "metadata": term_metadata}}
)
return wrapped_func(plugin, **kwargs)

return wrapper
26 changes: 25 additions & 1 deletion plugins/gbif/config.ini
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[Generic]
doi_url = https://doi.org/
api_config = /FAIR_eva/fair-api.yaml
api_config = fair-api.yaml
endpoint= https://api.gbif.org/v1
[local]
only_local = false
Expand Down Expand Up @@ -47,6 +47,30 @@ terms_access = [['access', ''], ['rights', '']]
# Accepted access protocols
terms_access_protocols =['http','https','ftp']

# Manual metadata access
metadata_access_manual = ['TODO']

# Manual data access
data_access_manual = ['TODO']

#Policy of metadata persistence
metadata_persistence = []

#Authentication for EPOS
metadata_authentication = []

#terms that use vocabularies and vocabularies used
dict_vocabularies= {'ROR': 'https://ror.org/', 'PIC': 'https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/how-to-participate/participant-register', 'imtypes': 'https://www.iana.org/assignments/media-types/media-types.xhtml', 'TRL': 'TRL', 'temporal': 'https://www.iso.org/iso-8601-date-and-time-format.html', 'Rolecode': 'Rolecode', 'spdx': 'https://spdx.org/licenses/', 'ORCID': 'https://orcid.org/'}

terms_vocabularies=[['identifiers','relatedDataProducts'],
['',''],
['availableFormats',''],
['',''],
['temporalCoverage','relatedDataProducts'],#no temporal metatdata
['',''],
['license',''],
['contactPoints','relatedDataProducts']]

# Metadata terms wich includes controlled vocabularies. More controlled vocabularies can be imlpemented in plugins
terms_cv = [['coverage', 'spatial'], ['subject', 'lcsh']]

Expand Down
Loading

0 comments on commit 7ddf874

Please sign in to comment.