Merge pull request #196 from IFB-ElixirFr/new-terms

v1.2.3 new terms button

app.py

@@ -814,8 +814,7 @@ def evaluate_fairmetrics(json, metric_name, client_metric_id, url):
 
 
 def evaluate_fc_metrics(metric_name, client_metric_id, url):
-    # print("OK FC Metrics")
-    # print(cache.get("TOTO"))
+    # print(metric_name)
     # print(METRICS_CUSTOM)
 
     dev_logger.info("Evaluating FAIR-Checker metric")
@@ -880,7 +879,6 @@ def evaluate_fc_metrics(metric_name, client_metric_id, url):
         # "name": name,
     }
     emit("done_" + client_metric_id, emit_json)
-    dev_logger.info("DONE our own metric !")
 
 
 @socketio.on("quick_structured_data_search")

metrics/A12_Impl.py

@@ -0,0 +1,77 @@
+from metrics.AbstractFAIRMetrics import AbstractFAIRMetrics
+import validators
+from metrics.recommendation import json_rec
+
+
+class A12_Impl(AbstractFAIRMetrics):
+    """
+    GOAL : retrieve embedded semantic annotations
+    """
+
+    def __init__(self, web_resource=None):
+        super().__init__(web_resource)
+        self.name = "Authorisation procedure or access rights"
+        self.id = "16"
+        self.principle = "https://w3id.org/fair/principles/terms/A1.2"
+        self.principle_tag = "A1.2"
+        self.implem = "FAIR-Checker"
+        self.desc = """
+            The protocol allows for an authentication and authorisation procedure where necessary. <br>
+            FAIR-Checker verifies if access rights are specified in metadata through terms 
+            odrl:hasPolicy, dct:rights, dct:accessRights, or dct:license. 
+        """
+
+    def weak_evaluate(self):
+        eval = self.get_evaluation()
+        eval.set_implem(self.implem)
+        eval.set_metrics(self.principle_tag)
+        return eval
+
+    def strong_evaluate(self):
+        eval = self.get_evaluation()
+        eval.set_implem(self.implem)
+        eval.set_metrics(self.principle_tag)
+
+        checked_properties = """
+            odrl:hasPolicy
+            dct:rights
+            dct:accessRights
+            dct:license
+            schema:license
+        """
+        query_prov = (
+            self.COMMON_SPARQL_PREFIX
+            + """ 
+ASK { 
+    VALUES ?p { """
+            + checked_properties
+            + """ } . 
+    ?s ?p ?o .
+}
+            """
+        )
+
+        eval.log_info(
+            "Checking that at least one of the access policy properties is found in metadata:\n"
+            + checked_properties
+        )
+        res = self.get_web_resource().get_rdf().query(query_prov)
+        for bool_res in res:
+            if bool_res:
+                eval.log_info(
+                    "At least one of the access policy properties was found in metadata !"
+                )
+                eval.set_score(2)
+                return eval
+            else:
+                eval.log_info(
+                    "None of the access policy properties were found in metadata !"
+                )
+                eval.set_recommendations(
+                    json_rec["A12"]["reco1"]
+                    + checked_properties
+                    + """
+                """
+                )
+                eval.set_score(0)
+                return eval

metrics/AbstractFAIRMetrics.py

@@ -1,15 +1,14 @@
 from abc import ABC, abstractmethod
 import logging
-import sys
-from io import StringIO
-from metrics.Evaluation import Result, Evaluation
+from metrics.Evaluation import Evaluation
 
 
 class AbstractFAIRMetrics(ABC):
 
     COMMON_SPARQL_PREFIX = """
 PREFIX schema: <http://schema.org/>
 PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX dcat: <http://www.w3.org/ns/dcat#>
 PREFIX doap: <http://usefulinc.com/ns/doap#>
 PREFIX dbpedia-owl: <http://dbpedia.org/ontology/>
 PREFIX cc: <http://creativecommons.org/ns#>
@@ -19,6 +18,7 @@ class AbstractFAIRMetrics(ABC):
 PREFIX prov: <http://www.w3.org/ns/prov#>
 PREFIX pav: <http://purl.org/pav/>
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+PREFIX odrl: <http://www.w3.org/ns/odrl/2/>
     """
 
     cache = {}

metrics/F1A_Impl.py

@@ -1,18 +1,7 @@
 import logging
-import json
-
-import requests
-from pathlib import Path
-from urllib.parse import urlparse
-import logging
-from rdflib import URIRef
 
 from metrics.AbstractFAIRMetrics import AbstractFAIRMetrics
-from datetime import timedelta
-from metrics.FairCheckerExceptions import FairCheckerException
 from metrics.Evaluation import Evaluation
-import validators
-import re
 from metrics.recommendation import json_rec
 
 
@@ -31,8 +20,7 @@ def __init__(self, web_resource=None):
         self.principle_tag = "F1A"
         self.implem = "FAIR-Checker"
         self.desc = """
-            FAIRChecker check that the resource identifier is an URL that can be reach, meaning it is unique, it is even
-             better if the URL refer to a DOI.
+FAIRChecker checks that the resource identifier is a reachable URL. It's better if the URL is persistent (WebID, PURL or DOI).   
         """
 
     def weak_evaluate(self, eval=None) -> Evaluation:

metrics/F2A_Impl.py

@@ -28,17 +28,12 @@ def __init__(self, web_resource=None):
         self.principle_tag = "F2A"
         self.implem = "FAIR-Checker"
         self.desc = """
-            FAIR-Checker verifies that at least one RDF triple can be found in metadata. 
+            For weak assessment, FAIR-Checker verifies that at least one RDF triple can be found in metadata. 
+            For strong assessment, it searches for at least one property in dct:title dct:description dct:accessURL
+            dct:downloadURL dcat:endpointURL dcat:endpointDescription.    
         """
 
     def weak_evaluate(self, eval=None) -> Evaluation:
-        if not eval:
-            eval = self.get_evaluation()
-            eval.set_implem(self.implem)
-            eval.set_metrics(self.principle_tag)
-        return eval
-
-    def strong_evaluate(self, eval=None) -> Evaluation:
         """
         at least one embedded RDF triple
         """
@@ -59,11 +54,71 @@ def strong_evaluate(self, eval=None) -> Evaluation:
                 + " RDF triples were found, thus data is in a well structured graph format"
             )
             # print(len(kg))
-            eval.set_score(2)
+            eval.set_score(1)
             return eval
         eval.log_info(
             "No RDF triples found, thus data is probably not structured as needed"
         )
         eval.set_recommendations(json_rec["F2A"]["reco1"])
         eval.set_score(0)
         return eval
+
+    def strong_evaluate(self, eval=None) -> Evaluation:
+
+        if not eval:
+            eval = self.get_evaluation()
+            eval.set_implem(self.implem)
+            eval.set_metrics(self.principle_tag)
+
+        checked_properties = """
+                    dct:title
+                    dct:description
+                    dcat:accessURL
+                    dcat:downloadURL
+                    dcat:endpointDescription
+                    dcat:endpointURL
+                """
+        query_prov = (
+            self.COMMON_SPARQL_PREFIX
+            + """ 
+        ASK { 
+            VALUES ?p { """
+            + checked_properties
+            + """ } . 
+            ?s ?p ?o .
+        }
+                    """
+        )
+
+        eval.log_info(
+            "Checking that at least one of the access policy properties is found in metadata:\n"
+            + checked_properties
+        )
+        res = self.get_web_resource().get_rdf().query(query_prov)
+        print()
+        print(res)
+        print()
+        for bool_res in res:
+            print(bool_res)
+            if bool_res:
+                eval.log_info(
+                    "At least one of the discoverability properties was found in metadata !"
+                )
+                eval.set_score(2)
+                return eval
+            else:
+                eval.log_info(
+                    "None of the discoverability properties were found in metadata !"
+                )
+                eval.set_recommendations(
+                    json_rec["F2A"]["reco2"]
+                    + checked_properties
+                    + """
+                        """
+                )
+                eval.set_score(0)
+                return eval
+
+        print("ERROR ERROR ERROR")
+        eval.set_score(0)
+        return eval

metrics/FAIRMetricsFactory.py

@@ -5,6 +5,7 @@
 from metrics.F2A_Impl import F2A_Impl
 from metrics.F2B_Impl import F2B_Impl
 from metrics.A11_Impl import A11_Impl
+from metrics.A12_Impl import A12_Impl
 from metrics.I1_Impl import I1_Impl
 from metrics.I1A_Impl import I1A_Impl
 from metrics.I1B_Impl import I1B_Impl
@@ -42,6 +43,7 @@ def get_FC_metrics():
             F2A_Impl().get_name(): F2A_Impl(),
             F2B_Impl().get_name(): F2B_Impl(),
             A11_Impl().get_name(): A11_Impl(),
+            A12_Impl().get_name(): A12_Impl(),
             I1_Impl().get_name(): I1_Impl(),
             I2_Impl().get_name(): I2_Impl(),
             I3_Impl().get_name(): I3_Impl(),
@@ -59,6 +61,7 @@ def get_FC_impl(web_resource=None):
             F2A_Impl(web_resource),
             F2B_Impl(web_resource),
             A11_Impl(web_resource),
+            A12_Impl(web_resource),
             I1_Impl(web_resource),
             I2_Impl(web_resource),
             I3_Impl(web_resource),
@@ -103,6 +106,13 @@ def get_A11(web_resource, impl=Implem.FAIR_CHECKER):
         else:
             return A11_Impl(web_resource)
 
+    @staticmethod
+    def get_A12(web_resource, impl=Implem.FAIR_CHECKER):
+        if impl == Implem.FAIR_METRICS_API:
+            raise NotYetImplementedException
+        else:
+            return A12_Impl(web_resource)
+
     @staticmethod
     def get_I1(web_resource, impl=Implem.FAIR_CHECKER):
         if impl == Implem.FAIR_METRICS_API:

metrics/I1A_Impl.py

@@ -16,7 +16,7 @@ def __init__(self, web_resource=None):
         self.principle_tag = "I1A"
         self.implem = "FAIR-Checker"
         self.desc = """
-            FAIR-Checker verifies that at least one RDF triple can be found in metadata. 
+            For the strong assessment, FAIR-Checker verifies that at least one RDF triple can be found in metadata.  
         """
 
     def weak_evaluate(self):
@@ -31,7 +31,7 @@ def weak_evaluate(self):
 
     def strong_evaluate(self):
         """
-        Delegated to F2B
+        Delegated to F2A
         """
         eval = self.get_evaluation()
         eval.set_implem(self.implem)

metrics/I1_Impl.py

@@ -27,8 +27,8 @@ def weak_evaluate(self):
         Delegated to F2A
         """
         eval = self.get_evaluation()
-        eval.set_implem(self.implem)
-        eval.set_metrics(self.principle_tag)
+        # eval.set_implem(self.implem)
+        # eval.set_metrics(self.principle_tag)
         eval_from_F2A = F2A_Impl(self.get_web_resource()).weak_evaluate(eval=eval)
         return eval_from_F2A
 
@@ -37,7 +37,7 @@ def strong_evaluate(self):
         Delegated to F2A
         """
         eval = self.get_evaluation()
-        eval.set_implem(self.implem)
-        eval.set_metrics(self.principle_tag)
+        # eval.set_implem(self.implem)
+        # eval.set_metrics(self.principle_tag)
         eval_from_F2A = F2A_Impl(self.get_web_resource()).strong_evaluate(eval=eval)
         return eval_from_F2A

metrics/R12_Impl.py

@@ -40,10 +40,13 @@ def strong_evaluate(self):
             prov:wasAssociatedWith
             prov:startedAtTime 
             prov:endedAtTime
-            dct:hasVersion 
+            dct:hasVersion
+            dct:isVersionOf 
             dct:creator 
             dct:contributor 
-            pav:hasVersion 
+            dct:publisher
+            pav:hasVersion
+            pav:version 
             pav:hasCurrentVersion 
             pav:createdBy 
             pav:authoredBy 
@@ -55,6 +58,11 @@ def strong_evaluate(self):
             pav:curatedBy 
             pav:createdAt 
             pav:previousVersion
+            schema:creator
+            schema:author
+            schema:publisher
+            schema:provider
+            schema:funder
         """
         query_prov = (
             self.COMMON_SPARQL_PREFIX