Merge pull request #90 from xgaia/release_3.2.4

Release 3.2.4

.travis.yml

@@ -16,17 +16,17 @@ matrix:
       - docker pull askomics/virtuoso:7.2.5.1
       - docker pull bgruening/galaxy-stable:19.01
       - docker pull xgaia/corese:latest
-      - docker pull xgaia/isql-api:2.1.0
+      - docker pull xgaia/isql-api:2.1.1
       - sudo docker run -d --name virtuoso -p 8891:8890 -p 1112:1111 -e DBA_PASSWORD=dba -e SPARQL_UPDATE=true -e DEFAULT_GRAPH=http://localhost:8891/DAV -t askomics/virtuoso:7.2.5.1 /bin/sh -c "netstat -nr | grep '^0\.0\.0\.0' | grep -oE '((1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])\.){3}(1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])' | grep -v '^0\.0\.0\.0' | sed 's/$/ askomics-host/' >> /etc/hosts && /virtuoso/virtuoso.sh"
       - sleep 1m
       - sudo docker run -d --name redis -p 6380:6379 -t redis:4.0
       - sudo docker run -d --name galaxy -p 8081:80 -t bgruening/galaxy-stable:19.01
       - sudo docker run -d --name corese -p 8082:8080 -t xgaia/corese:latest /bin/sh -c "netstat -nr | grep '^0\.0\.0\.0' | grep -oE '((1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])\.){3}(1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])' | grep -v '^0\.0\.0\.0' | sed 's/$/ askomics-host/' >> /etc/hosts && /corese/start.sh"
-      - sudo docker run -d --name isql-api -p 5051:5050 -e VIRTUOSO_HOST=askomics-host -e VIRTUOSO_ISQL_PORT=1112 -t xgaia/isql-api:2.1.0  /bin/sh -c "netstat -nr | grep '^0\.0\.0\.0' | grep -oE '((1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])\.){3}(1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])' | grep -v '^0\.0\.0\.0' | sed 's/$/ askomics-host/' >> /etc/hosts && sh /isqlapi/docker-run.sh"
+      - sudo docker run -d --name isql-api -p 5051:5050 -e VIRTUOSO_HOST=askomics-host -e VIRTUOSO_ISQL_PORT=1112 -t xgaia/isql-api:2.1.1  /bin/sh -c "netstat -nr | grep '^0\.0\.0\.0' | grep -oE '((1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])\.){3}(1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])' | grep -v '^0\.0\.0\.0' | sed 's/$/ askomics-host/' >> /etc/hosts && sh /isqlapi/docker-run.sh"
       - sleep 1m
       script:
         - flake8 askomics tests --ignore=E501,W504
-        - pytest --cov=. -vv --log-cli-level debug
+        - pytest --cov=. -vv
       after_success:
         coveralls
 

askomics/libaskomics/SparqlQueryBuilder.py

@@ -259,7 +259,7 @@ def toggle_public(self, graph, public):
         '''.format(graph=graph, public=public)
 
         query_launcher = SparqlQueryLauncher(self.app, self.session)
-        query_launcher.execute_query(self.prefix_query(query), no_isql=True)
+        query_launcher.execute_query(self.prefix_query(query))
 
     def get_default_query_with_prefix(self):
         """Get default query with the prefixes

askomics/libaskomics/SparqlQueryLauncher.py

@@ -230,7 +230,7 @@ def insert_data(self, ttl, graph, metadata=False):
         }}
         '''.format(graph, triples)
 
-        return self.execute_query(query, no_isql=True)
+        return self.execute_query(query)
 
     def drop_dataset(self, graph):
         """Drop the datasets of the triplestore and its metadata
@@ -243,9 +243,9 @@ def drop_dataset(self, graph):
         query = '''
         DROP SILENT GRAPH <{}>
         '''.format(graph)
-        self.execute_query(query, disable_log=True)
+        self.execute_query(query, disable_log=True, isql_api=True)
 
-    def process_query(self, query, no_isql=False):
+    def process_query(self, query, isql_api=False):
         """Execute a query and return parsed results
 
         Parameters
@@ -258,9 +258,9 @@ def process_query(self, query, no_isql=False):
         list
             Parsed results
         """
-        return self.parse_results(self.execute_query(query, no_isql=False))
+        return self.parse_results(self.execute_query(query, isql_api=isql_api))
 
-    def execute_query(self, query, disable_log=False, no_isql=False):
+    def execute_query(self, query, disable_log=False, isql_api=False):
         """Execute a sparql query
 
         Parameters
@@ -274,15 +274,15 @@ def execute_query(self, query, disable_log=False, no_isql=False):
             result
         """
         try:
+            triplestore = self.settings.get("triplestore", "triplestore")
 
             # Use ISQL or SPARQL
-            triplestore = self.settings.get("triplestore", "triplestore")
-            isqlapi = None
+            isql_api_url = None
             try:
-                isqlapi = self.settings.get("triplestore", "isqlapi")
+                isql_api_url = self.settings.get("triplestore", "isqlapi")
             except Exception:
                 pass
-            use_isql = True if triplestore == "virtuoso" and isqlapi and self.local_query and not no_isql else False
+            use_isql = True if triplestore == "virtuoso" and isql_api_url and self.local_query and isql_api else False
 
             start_time = time.time()
             self.endpoint.setQuery(query)
@@ -295,7 +295,7 @@ def execute_query(self, query, disable_log=False, no_isql=False):
             if use_isql:
                 formatted_query = "SPARQL {}".format(query)
                 json = {"command": formatted_query, "disable_log": disable_log, "sparql_select": not self.endpoint.isSparqlUpdateRequest()}
-                response = requests.post(url=isqlapi, json=json)
+                response = requests.post(url=isql_api_url, json=json)
                 results = response.json()
                 if results["status"] == 500:
                     raise HTTPError("isqlapi: {}".format(results["message"]))

askomics/tasks.py

@@ -165,7 +165,7 @@ def query(self, session, info):
         results = []
         if query_builder.graphs:
             query_launcher = SparqlQueryLauncher(app, session, get_result_query=True, federated=federated, endpoints=endpoints)
-            headers, results = query_launcher.process_query(query)
+            headers, results = query_launcher.process_query(query, isql_api=True)
 
         # write result to a file
         file_size = result.save_result_in_file(headers, results)
@@ -215,7 +215,7 @@ def sparql_query(self, session, info):
         result.update_db_status("started", update_celery=True)
 
         query_launcher = SparqlQueryLauncher(app, session, get_result_query=True, federated=info["federated"], endpoints=info["endpoints"])
-        header, data = query_launcher.process_query(info["sparql_query"])
+        header, data = query_launcher.process_query(info["sparql_query"], isql_api=True)
 
         # Write results in file
         file_size = result.save_result_in_file(header, data)

package.json

@@ -8,7 +8,7 @@
     "ontology"
   ],
   "name": "AskOmics",
-  "version": "3.2.3",
+  "version": "3.2.4",
   "description": "Visual SPARQL query builder",
   "author": "Xavier Garnier",
   "license": "AGPL-3.0",

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='askomics',
-    version='3.2.3',
+    version='3.2.4',
     description='''
         AskOmics is a visual SPARQL query interface supporting both intuitive
         data integration and querying while shielding the user from most of the