Api bioschemas profile validation

app.py

@@ -610,6 +610,20 @@ def get(self):
         return check_kg(kg, True)
 
 
+@fc_inspect_namespace.route("/bioschemas_validation")
+class InspectBioschemas(Resource):
+    @fc_inspect_namespace.expect(reqparse)
+    def get(self):
+        """Validate an RDF JSON-LD graph against Bioschemas profiles"""
+        args = reqparse.parse_args()
+        url = args["url"]
+
+        web_res = WebResource(url)
+        kg = web_res.get_rdf()
+        results = validate_any_from_KG(kg)
+        return results
+
+
 def list_routes():
     return ["%s" % rule for rule in app.url_map.iter_rules()]
 

tests/test_API.py

@@ -114,3 +114,10 @@ def test_inspect_ontologies(self):
         self.assertEqual(200, response.status_code)
         self.assertEqual(3, len(response.get_json()["classes"]))
         self.assertEqual(14, len(response.get_json()["properties"]))
+
+    def test_inspect_bioschemas(self):
+        response = self.app.get(
+            "/api/inspect/bioschemas_validation?url=" + self.url_biotools,
+        )
+        self.assertEqual(200, response.status_code)
+        self.assertLess(0, len(response.get_json()))

tests/test_gen_shacl.py

@@ -91,15 +91,15 @@ def test_biotools_validation(self):
             input_url="https://bio.tools/api/jaspar?format=jsonld", rdf_syntax="json-ld"
         )
         self.assertGreater(len(res), 0)
-        self.assertEquals(len(res["https://bio.tools/jaspar"]["warnings"]), 5)
-        self.assertEquals(len(res["https://bio.tools/jaspar"]["errors"]), 3)
+        self.assertEqual(len(res["https://bio.tools/jaspar"]["warnings"]), 5)
+        self.assertEqual(len(res["https://bio.tools/jaspar"]["errors"]), 3)
 
     def test_pangaea_validation(self):
         res = validate_any_from_microdata(
             input_url="https://doi.pangaea.de/10.1594/PANGAEA.914331"
         )
         self.assertGreater(len(res[0]), 0)
-        self.assertEquals(
+        self.assertEqual(
             len(res[0]["https://doi.org/10.1594/PANGAEA.914331"]["errors"]), 0
         )
 
@@ -109,10 +109,10 @@ def test_datacite_validation(self):
         )
         self.assertGreater(len(res[0]), 0)
         self.assertFalse(res[0]["https://doi.org/10.7892/boris.108387"]["conforms"])
-        self.assertEquals(
+        self.assertEqual(
             len(res[0]["https://doi.org/10.7892/boris.108387"]["errors"]), 2
         )
-        self.assertEquals(
+        self.assertEqual(
             len(res[0]["https://doi.org/10.7892/boris.108387"]["warnings"]), 11
         )
 
@@ -126,8 +126,8 @@ def test_datacite_validation_kg(self):
         res = validate_any_from_KG(kg=kg)
         self.assertGreater(len(res), 0)
         self.assertFalse(res["https://doi.org/10.7892/boris.108387"]["conforms"])
-        self.assertEquals(len(res["https://doi.org/10.7892/boris.108387"]["errors"]), 2)
-        self.assertEquals(
+        self.assertEqual(len(res["https://doi.org/10.7892/boris.108387"]["errors"]), 2)
+        self.assertEqual(
             len(res["https://doi.org/10.7892/boris.108387"]["warnings"]), 11
         )
 

tests/test_vocab.py

@@ -226,7 +226,7 @@ def test_exclude_ns_prefix(self):
         print("toto")
         print(len(kg))
         print(len(cleaned_kg))
-        self.assertEquals(len(kg) - 2, len(cleaned_kg))
+        self.assertEqual(len(kg) - 2, len(cleaned_kg))
 
     def test_exclude_xhtml(self):
         ns = "http://www.w3.org/1999/xhtml/vocab#"
@@ -246,7 +246,7 @@ def test_exclude_xhtml(self):
         print(q_xhtml)
 
         res = kg.query(q_xhtml)
-        self.assertEquals(len(res), 1)
+        self.assertEqual(len(res), 1)
 
         q_del = (
             'DELETE {?s ?p ?o} WHERE { ?s ?p ?o . FILTER (strstarts(str(?p), "'
@@ -257,7 +257,7 @@ def test_exclude_xhtml(self):
         print(kg.serialize(format="turtle"))
 
         res = kg.query(q_xhtml)
-        self.assertEquals(len(res), 0)
+        self.assertEqual(len(res), 0)
 
 
 if __name__ == "__main__":