Fix anonymous access & prepare 4.4

CHANGELOG.md

@@ -14,6 +14,7 @@ This changelog was started for release 4.2.0.
 - Fixed an issue with forms (missing field and entity name for label & uri fields) (Issue #255)
 - Fixed an issue with the data endpoint for FALDO entities (Issue #279)
 - Fixed an issue where integration would fail when setting a category type on a empty column (#334)
+- Fixed an issue with saved queries for non-logged users
 
 ### Added
 
@@ -28,12 +29,15 @@ This changelog was started for release 4.2.0.
 - Add better error management for RDF files
 - Added 'single tenant' mode: Send queries to all graphs to speed up
 - Added ontologies management
+- Added prefixes management
+- Added 'external graph' management for federated request: federated requests will only target this remote graph
+- Added support for multithread in web server, with the *WORKERS* env variable when calling make
 
 ### Changed
 
 - Changed "Query builder" to "Form editor" in form editing interface
-- Changed abstraction building method for relations. (Please refer to #248 and #268)
-- Changed abstraction building method for attributes. (Please refer to #321 and #324)
+- Changed abstraction building method for relations. (Please refer to #248 and #268). Correct 'phantom' relations
+- Changed abstraction building method for attributes. (Please refer to #321 and #324). Correct 'attributes' relations
 - Changed abstraction building method for 'strand': only add the required strand type, and not all three types (#277)
 - Updated documentation
 - Changed the sparql endpoint: now use the authenticated SPARQL endpoint instead of public endpoint. Write permissions are not required anymore

Makefile

@@ -9,6 +9,7 @@ FLASKOPTS=
 PYTESTOPTS=
 TESTFILE?=tests
 NTASKS?=1
+WORKERS?=1
 
 HOST?=0.0.0.0
 PORT?=5000
@@ -52,20 +53,20 @@ help:
 	@echo '    make clean                                                         Uninstall everything'
 	@echo '    make install [MODE=dev]                                            Install Python and Js dependencies (+ dev dependencies if MODE=dev)'
 	@echo '    make build [MODE=dev]                                              Build javascript (and watch for update if MODE=DEV)'
-	@echo '    make serve [MODE=dev] [HOST=0.0.0.0] [PORT=5000] [NTASKS=1]        Serve AskOmics at $(HOST):$(PORT)'
+	@echo '    make serve [MODE=dev] [HOST=0.0.0.0] [PORT=5000] [NTASKS=1] [WORKERS=1] Serve AskOmics at $(HOST):$(PORT)'
 	@echo '    make test                                                          Lint and test javascript and python code'
 	@echo '    make serve-doc [DOCPORT=8000]                                      Serve documentation at localhost:$(DOCPORT)'
 	@echo '    make update-base-url                                               Update all graphs from an old base_url to a new base_url'
 	@echo '    make clear-cache                                                   Clear abstraction cache'
 	@echo ''
 	@echo 'Examples:'
-	@echo '    make clean install build serve NTASKS=10                           Clean install and serve AskOmics in production mode, 10 celery tasks in parallel'
-	@echo '    make clean install serve MODE=dev NTASKS=10                        Clean install and serve AskOmics in development mode, 10 celery tasks in parallel'
+	@echo '    make clean install build serve NTASKS=10 WORKERS=2                 Clean install and serve AskOmics in production mode, 10 celery tasks in parallel, 2 workers on the web server'
+	@echo '    make clean install serve MODE=dev NTASKS=10 WORKERS=2              Clean install and serve AskOmics in development mode, 10 celery tasks in parallel, 2 workers on the web server'
 	@echo ''
 	@echo '    make clean install                                                 Clean install AskOmics'
 	@echo '    make clean install  MODE=dev                                       Clean install AskOmics in development mode'
-	@echo '    make serve NTASKS=10                                               Serve AskOmics, 10 celery tasks in parallel'
-	@echo '    make serve MODE=dev NTASKS=10                                      Serve AskOmics in development mode, 10 celery tasks in parallel'
+	@echo '    make serve NTASKS=10 WORKERS=2                                     Serve AskOmics, 10 celery tasks in parallel, 2 workers on the web server'
+	@echo '    make serve MODE=dev NTASKS=10 WORKERS=2                            Serve AskOmics in development mode, 10 celery tasks in parallel, 2 workers on the web server'
 	@echo ''
 	@echo '    make pytest MODE=dev TESTFILE=tests/test_api.py                    Test tests/test_api file only'
 
@@ -106,7 +107,7 @@ serve-askomics: check-venv build-config create-user
 ifeq ($(MODE), dev)
 	FLASK_ENV=development FLASK_APP=app flask run --host=$(HOST) --port $(PORT)
 else
-	FLASK_ENV=production FLASK_APP=app gunicorn -b $(HOST):$(PORT) app
+	FLASK_ENV=production FLASK_APP=app gunicorn -w $(WORKERS) -b $(HOST):$(PORT) app
 endif
 
 serve-celery: check-venv build-config create-user

askomics/api/results.py

@@ -14,6 +14,8 @@
 
 
 def can_access(user):
+    if not user:
+        return False
     login_allowed = current_app.iniconfig.getboolean('askomics', 'enable_sparql_console', fallback=False)
     return login_allowed or user['admin']
 
@@ -166,7 +168,7 @@ def get_graph_and_sparql_query():
         # Get all graphs and endpoint, and mark as selected the used one
         query = SparqlQuery(current_app, session, get_graphs=True)
         graphs, endpoints = query.get_graphs_and_endpoints(selected_graphs=graphs, selected_endpoints=endpoints)
-        console_enabled = can_access(session['user'])
+        console_enabled = can_access(session.get('user'))
 
     except Exception as e:
         traceback.print_exc(file=sys.stdout)

askomics/libaskomics/OntologyManager.py

@@ -261,15 +261,19 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
                 "fieldList": "label"
             }
 
-            r = requests.get(base_url, params=arguments)
-
             data = []
 
-            if not r.status_code == 200:
-                return data
+            try:
+                r = requests.get(base_url, params=arguments, timeout=10)
+
+                if not r.status_code == 200:
+                    return data
+
+                res = r.json()
+                if res['response']['docs']:
+                    data = [term['label'] for term in res['response']['docs']]
 
-            res = r.json()
-            if res['response']['docs']:
-                data = [term['label'] for term in res['response']['docs']]
+            except requests.exceptions.Timeout:
+                pass
 
             return data

askomics/react/src/routes/query/ontolinkview.jsx

@@ -31,7 +31,7 @@ export default class OntoLinkView extends Component {
                 <option selected={this.props.link.uri == '^http://www.w3.org/2000/01/rdf-schema#subClassOf*' ? true : false} value="^http://www.w3.org/2000/01/rdf-schema#subClassOf*">ancestors of</option>
               </CustomInput>
             </td>
-            <td> a term</td>
+            <td>&nbsp;a term</td>
           </tr>
         </table>
         <br />

askomics/react/src/routes/query/query.jsx

@@ -559,7 +559,7 @@ export default class Query extends Component {
               target: targetId,
               selected: false,
               suggested: true,
-              directed: isOnto ? false : true,
+              directed: true,
             })
             incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
           }
@@ -703,7 +703,7 @@ export default class Query extends Component {
           target: node1.id,
           selected: false,
           suggested: false,
-          directed: link.direct,
+          directed: link.directed,
         }
       }
     })
@@ -1345,10 +1345,10 @@ export default class Query extends Component {
 
   getOntoLabel (uri) {
       let labels = {}
-      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "Children of"
-      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "Descendants of"
-      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "Parents of"
-      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "Ancestors of"
+      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "is children of"
+      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "is descendant of"
+      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "is parents of"
+      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "is ancestor of"
       return labels[uri]
   }
 

askomics/static/about.html

@@ -12,7 +12,7 @@ <h4>What is AskOmics?</h4>
   Visit <a target="_newtab" rel="noopener noreferrer" href="https://askomics.org">askomics.org</a> to learn how to use and deploy AskOmics.
 </p>
 
-<h4>Usefull links</h4>
+<h4>Useful links</h4>
 <p>
   <div>
     <a target="_newtab" rel="noopener noreferrer" href="https://flaskomics.readthedocs.io">Docs</a>

config/askomics.ini.template

@@ -132,9 +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