Merge branch 'dev_onto_clean' of github.com:mboudet/flaskomics into d…

…ev_onto_clean

askomics/api/ontology.py

@@ -1,6 +1,6 @@
 import traceback
 import sys
-from askomics.api.auth import api_auth, login_required
+from askomics.api.auth import api_auth
 from askomics.libaskomics.OntologyManager import OntologyManager
 
 from flask import (Blueprint, current_app, jsonify, request, session)
@@ -10,7 +10,6 @@
 
 @onto_bp.route("/api/ontology/<short_ontology>/autocomplete", methods=["GET"])
 @api_auth
-@login_required
 def autocomplete(short_ontology):
     """Get the default sparql query
 
@@ -19,8 +18,13 @@ def autocomplete(short_ontology):
     json
     """
 
+    if "user" not in session and current_app.iniconfig.getboolean("askomics", "protect_public"):
+        return jsonify({
+            "error": True,
+            "errorMessage": "Ontology {} not found".format(short_ontology),
+            "results": []
+        }), 401
     try:
-        # Disk space
         om = OntologyManager(current_app, session)
         ontology = om.get_ontology(short_name=short_ontology)
         if not ontology:
@@ -45,7 +49,7 @@ def autocomplete(short_ontology):
             "error": True,
             "errorMessage": str(e),
             "results": []
-        }), 404
+        }), 500
 
     return jsonify({
         "error": False,

config/askomics.ini.template

@@ -83,6 +83,10 @@ ldap_mail_attribute = mail
 #ldap_password_reset_link =
 #ldap_account_link =
 
+# Max results returned for autocompletion
+autocomplete_max_results = 10
+
+
 [triplestore]
 # name of the triplestore, can be virtuoso or fuseki
 triplestore = virtuoso
@@ -128,9 +132,6 @@ preview_limit = 25
 # All queries are launched on all graphes (speedup queries)
 single_tenant=False
 
-# Max results returned for autocompletion
-autocomplete_max_results = 10
-
 [federation]
 # Query engine can be corese or fedx
 #query_engine = corese

config/askomics.test.ini

@@ -76,6 +76,7 @@ ldap_surname_attribute = sn
 ldap_mail_attribute = mail
 #ldap_password_reset_link =
 #ldap_account_link =
+autocomplete_max_results = 20
 
 [triplestore]
 # name of the triplestore, can be virtuoso or fuseki
@@ -132,3 +133,5 @@ local_endpoint=http://askomics-host:8891/sparql
 # Sentry dsn to report python and js errors in a sentry instance
 # server_dsn = https://00000000000000000000000000000000@exemple.org/1
 # frontend_dsn = https://00000000000000000000000000000000@exemple.org/2
+
+# Max results returned for autocompletion

tests/conftest.py

@@ -294,7 +294,7 @@ def upload_file_url(self, file_url):
         files.download_url(file_url, "1")
         return files.date
 
-    def integrate_file(self, info, public=False, set_graph=False):
+    def integrate_file(self, info, public=False, set_graph=False, graph=""):
         """Summary
 
         Parameters
@@ -310,6 +310,9 @@ def integrate_file(self, info, public=False, set_graph=False):
         files_handler = FilesHandler(self.app, self.session)
         files_handler.handle_files([info["id"], ])
 
+        # TODO: Fix this. Why do we need the virtuoso url?
+        graph = graph or "http://virtuoso:8890/sparql"
+
         for file in files_handler.files:
 
             dataset_info = {
@@ -321,7 +324,7 @@ def integrate_file(self, info, public=False, set_graph=False):
             }
 
             dataset = Dataset(self.app, self.session, dataset_info)
-            dataset.save_in_db("http://virtuoso:8890/sparql", set_graph=set_graph)
+            dataset.save_in_db(graph, set_graph=set_graph)
 
             if file.type == "csv/tsv":
                 file.integrate(dataset.id, info["columns_type"], public=public)
@@ -463,17 +466,15 @@ def upload_and_integrate_ontology(self):
         # integrate
         int_ontology = self.integrate_file({
             "id": 1,
-        })
+        }, set_graph=True, graph="http://localhost:8891/sparql-auth")
 
         return {
-            "ontology": {
-                "upload": up_ontology,
-                "timestamp": int_ontology["timestamp"],
-                "start": int_ontology["start"],
-                "end": int_ontology["end"],
-                "graph": int_ontology["graph"],
-                "endpoint": int_ontology["endpoint"]
-            },
+            "upload": up_ontology,
+            "timestamp": int_ontology["timestamp"],
+            "start": int_ontology["start"],
+            "end": int_ontology["end"],
+            "graph": int_ontology["graph"],
+            "endpoint": int_ontology["endpoint"]
         }
 
     def create_result(self, has_form=False):
@@ -623,7 +624,7 @@ def create_ontology(self):
         """Create ontology"""
         data = self.upload_and_integrate_ontology()
         om = OntologyManager(self.app, self.session)
-        om.add_ontology("AgrO ontology", "http://purl.obolibrary.org/obo/agro.owl", "AGRO", 1, data["graph"], "local")
+        om.add_ontology("AgrO ontology", "http://purl.obolibrary.org/obo/agro.owl", "AGRO", 1, data["graph"], data['endpoint'], "local")
         return data["graph"], data["endpoint"]
 
     @staticmethod

tests/test_api_admin.py

@@ -640,9 +640,9 @@ def test_add_ontology(self, client):
         assert response.status_code == 401
 
         client.log_user("jdoe")
-        data = client.upload_and_integrate_ontology()
-        graph = data["graph"]
-        endpoint = data["endpoint"]
+        graph_data = client.upload_and_integrate_ontology()
+        graph = graph_data["graph"]
+        endpoint = graph_data["endpoint"]
 
         response = client.client.post('/api/admin/addontology', json=data)
 
@@ -660,7 +660,7 @@ def test_add_ontology(self, client):
                 "id": 1,
                 "name": "AgrO ontology",
                 "uri": "http://purl.obolibrary.org/obo/agro.owl",
-                "short_name": "OBO",
+                "short_name": "AGRO",
                 "type": "local",
                 "dataset_id": 1,
                 "dataset_name": "agro_min.ttl",

tests/test_api_ontology.py

@@ -4,6 +4,23 @@
 class TestApiOntology(AskomicsTestCase):
     """Test AskOmics API /api/ontology/<someting>"""
 
+    def test_local_autocompletion_protected(self, client):
+        """ Test autocompletion on missing ontology"""
+        query = "blabla"
+        client.set_config("askomics", "protect_public", "true")
+        response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
+
+        assert response.status_code == 401
+        assert len(response.json["results"]) == 0
+
+    def test_local_autocompletion_missing_ontology(self, client):
+        """ Test autocompletion on missing ontology"""
+        query = "blabla"
+        response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
+
+        assert response.status_code == 404
+        assert len(response.json["results"]) == 0
+
     def test_local_autocompletion(self, client):
         """test /api/ontology/AGRO/autocomplete route"""
         client.create_two_users()
@@ -31,12 +48,17 @@ def test_local_autocompletion(self, client):
             "no-till",
             "puddling process",
             "mulch-till",
-            "ridge-till"
+            "ridge-till",
+            "strip-till",
+            "aerial application"
         ]
 
         assert response.status_code == 200
-        assert len(response.json["results"]) == 10
-        assert response.json["results"] == expected
+        assert len(response.json["results"]) == 12
+
+        # SPARQL order is not reliable, so we make sure to return everything
+        # If it fails, skip this
+        assert self.equal_objects(response.json["results"], expected)
 
         query = "irrigation"
         response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
@@ -48,4 +70,4 @@ def test_local_autocompletion(self, client):
 
         assert response.status_code == 200
         assert len(response.json["results"]) == 2
-        assert response.json["results"] == expected
+        assert self.equal_objects(response.json["results"], expected)