Merge 4c688a0 into 93f7434

CHANGELOG.md

@@ -24,6 +24,7 @@ This changelog was started for release 4.2.0.
 - Added 'Status' for files (for celery upload, and later for better file management)
 - Added tooltips to buttons in the query form (and other forms)
 - Added owl integration
+- Added 'single tenant' mode
 
 ### Changed
 
@@ -46,7 +47,7 @@ This changelog was started for release 4.2.0.
 - Bump path-parse from 1.0.6 to 1.0.7
 - Bump prismjs from 1.23.0 to 1.27.0
 - Bump simple-get from 2.8.1 to 2.8.2
-- Bump ssri from 6.0.1 to 6.0.2 
+- Bump ssri from 6.0.1 to 6.0.2
 - Bump follow-redirects from 1.14.4 to 1.14.8
 - Bump mkdocs from 1.0.4 to 1.2.3 in /docs
 - Bump python-ldap from 3.3.1 to 3.4.0

askomics/api/datasets.py

@@ -119,6 +119,7 @@ def toogle_public():
         error: True if error, else False
         errorMessage: the error message of error, else an empty string
     """
+
     data = request.get_json()
     if not (data and data.get("id")):
         return jsonify({

askomics/api/file.py

@@ -339,7 +339,7 @@ def integrate():
                 "file_id": file.id,
                 "name": file.human_name,
                 "graph_name": file.file_graph,
-                "public": data.get("public") if session["user"]["admin"] else False
+                "public": (data.get("public", False) if session["user"]["admin"] else False) or current_app.iniconfig.getboolean("askomics", "single_tenant", fallback=False)
             }
 
             dataset = Dataset(current_app, session, dataset_info)

askomics/api/start.py

@@ -79,7 +79,8 @@ def start():
             "namespaceInternal": current_app.iniconfig.get('triplestore', 'namespace_internal'),
             "proxyPath": proxy_path,
             "user": {},
-            "logged": False
+            "logged": False,
+            "singleTenant": current_app.iniconfig.getboolean('askomics', 'single_tenant', fallback=False)
         }
 
         json = {

askomics/libaskomics/SparqlQuery.py

@@ -1376,7 +1376,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
                     ))
                     var_to_replace.append((category_value_uri, var_2))
 
-        from_string = self.get_froms_from_graphs(self.graphs)
+        from_string = "" if self.settings.getboolean("askomics", "single_tenant", fallback=False) else self.get_froms_from_graphs(self.graphs)
         federated_from_string = self.get_federated_froms_from_graphs(self.graphs)
         endpoints_string = self.get_endpoints_string()
 

askomics/libaskomics/SparqlQueryLauncher.py

@@ -294,6 +294,7 @@ def execute_query(self, query, disable_log=False, isql_api=False):
 
             # Debug
             if self.settings.getboolean('askomics', 'debug'):
+                print(query)
                 self.log.debug("Launch {} query on {} ({})".format("ISQL" if use_isql else "SPARQL", self.triplestore, self.url_endpoint))
                 self.log.debug(query)
 

askomics/libaskomics/TriplestoreExplorer.py

@@ -208,12 +208,14 @@ def get_abstraction(self):
         """
         insert, abstraction = self.get_cached_asbtraction()
 
+        single_tenant = self.settings.getboolean("askomics", "single_tenant", fallback=False)
+
         # No abstraction entry in database, create it
         if not abstraction:
             abstraction = {
-                "entities": self.get_abstraction_entities(),
-                "attributes": self.get_abstraction_attributes(),
-                "relations": self.get_abstraction_relations()
+                "entities": self.get_abstraction_entities(single_tenant),
+                "attributes": self.get_abstraction_attributes(single_tenant),
+                "relations": self.get_abstraction_relations(single_tenant)
             }
 
             # Cache abstraction in DB, only for logged users
@@ -305,7 +307,7 @@ def uncache_abstraction(self, public=True, force=False):
 
             database.execute_sql_query(query, sql_var)
 
-    def get_abstraction_entities(self):
+    def get_abstraction_entities(self, single_tenant=False):
         """Get abstraction entities
 
         Returns
@@ -378,7 +380,7 @@ def get_abstraction_entities(self):
 
         return entities
 
-    def get_abstraction_attributes(self):
+    def get_abstraction_attributes(self, single_tenant=False):
         """Get user abstraction attributes from the triplestore
 
         Returns
@@ -497,7 +499,7 @@ def get_abstraction_attributes(self):
 
         return attributes
 
-    def get_abstraction_relations(self):
+    def get_abstraction_relations(self, single_tenant=False):
         """Get user abstraction relations from the triplestore
 
         Returns

askomics/react/src/routes.jsx

@@ -44,7 +44,8 @@ export default class Routes extends Component {
         gitUrl: null,
         disableIntegration: null,
         namespaceData: null,
-        namespaceInternal: null
+        namespaceInternal: null,
+        singleTenant: false
       }
     }
     this.cancelRequest

askomics/react/src/routes/integration/bedpreview.jsx

@@ -91,9 +91,12 @@ export default class BedPreview extends Component {
     if (this.state.publicTick) {
       publicIcon = <i className="fas fa-check text-success"></i>
     }
-
+    let privateButton
+    if (this.props.config.user.admin || !this.props.config.singleTenant){
+        privateButton = <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+    }
     let publicButton
-    if (this.props.config.user.admin) {
+    if (this.props.config.user.admin || this.props.config.singleTenant) {
       publicButton = <Button onClick={this.integrate} value="public" color="secondary" disabled={this.state.publicTick}>{publicIcon} Integrate (public dataset)</Button>
     }
 
@@ -124,7 +127,7 @@ export default class BedPreview extends Component {
           <br />
           <div className="center-div">
             <ButtonGroup>
-              <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+              {privateButton}
               {publicButton}
             </ButtonGroup>
             <br />

askomics/react/src/routes/integration/csvtable.jsx

@@ -240,9 +240,12 @@ export default class CsvTable extends Component {
     if (this.state.publicTick) {
       publicIcon = <i className="fas fa-check text-success"></i>
     }
-
+    let privateButton
+    if (this.props.config.user.admin || !this.props.config.singleTenant){
+        privateButton = <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+    }
     let publicButton
-    if (this.props.config.user.admin) {
+    if (this.props.config.user.admin || this.props.config.singleTenant) {
       publicButton = <Button onClick={this.integrate} value="public" color="secondary" disabled={this.state.publicTick}>{publicIcon} Integrate (public dataset)</Button>
     }
 
@@ -276,7 +279,7 @@ export default class CsvTable extends Component {
           <br />
           <div className="center-div">
             <ButtonGroup>
-              <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+              {privateButton}
               {publicButton}
             </ButtonGroup>
           </div>

askomics/react/src/routes/integration/gffpreview.jsx

@@ -100,8 +100,12 @@ export default class GffPreview extends Component {
     if (this.state.publicTick) {
       publicIcon = <i className="fas fa-check text-success"></i>
     }
+    let privateButton
+    if (this.props.config.user.admin || !this.props.config.singleTenant){
+        privateButton = <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+    }
     let publicButton
-    if (this.props.config.user.admin) {
+    if (this.props.config.user.admin || this.props.config.singleTenant) {
       publicButton = <Button onClick={this.integrate} value="public" color="secondary" disabled={this.state.publicTick}>{publicIcon} Integrate (public dataset)</Button>
     }
 
@@ -130,7 +134,7 @@ export default class GffPreview extends Component {
         <br />
           <div className="center-div">
             <ButtonGroup>
-              <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+              {privateButton}
               {publicButton}
             </ButtonGroup>
             <br />

askomics/react/src/routes/integration/rdfpreview.jsx

@@ -107,9 +107,12 @@ export default class RdfPreview extends Component {
     if (this.state.publicTick) {
       publicIcon = <i className="fas fa-check text-success"></i>
     }
-
+    let privateButton
+    if (this.props.config.user.admin || !this.props.config.singleTenant){
+        privateButton = <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+    }
     let publicButton
-    if (this.props.config.user.admin) {
+    if (this.props.config.user.admin || this.props.config.singleTenant) {
       publicButton = <Button onClick={this.integrate} value="public" color="secondary" disabled={this.state.publicTick}>{publicIcon} Integrate (public dataset)</Button>
     }
 
@@ -144,7 +147,7 @@ export default class RdfPreview extends Component {
         <br />
         <div className="center-div">
           <ButtonGroup>
-            <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+            {privateButton}
             {publicButton}
           </ButtonGroup>
         </div>

askomics/tasks.py

@@ -47,7 +47,7 @@ def integrate(self, session, data, host_url):
     files_handler = FilesHandler(app, session, host_url=host_url, external_endpoint=data["externalEndpoint"], custom_uri=data["customUri"])
     files_handler.handle_files([data["fileId"], ])
 
-    public = data.get("public", False) if session["user"]["admin"] else False
+    public = (data.get("public", False) if session["user"]["admin"] else False) or app.iniconfig.getboolean("askomics", "single_tenant", fallback=False)
 
     for file in files_handler.files:
 
@@ -170,7 +170,7 @@ def query(self, session, info):
 
         headers = info["selects"]
         results = []
-        if info["graphs"]:
+        if info["graphs"] or app.iniconfig.getboolean("askomics", "single_tenant", fallback=False):
             query_launcher = SparqlQueryLauncher(app, session, get_result_query=True, federated=info["federated"], endpoints=info["endpoints"])
             headers, results = query_launcher.process_query(info["query"], isql_api=True)
 

config/askomics.ini.template

@@ -124,6 +124,9 @@ preview_limit = 25
 # Triplestore max rows limit
 # result_set_max_rows = 10000
 
+# Single tenant means all graphs are public
+single_tenant=False
+
 [federation]
 # Query engine can be corese or fedx
 #query_engine = corese

config/askomics.test.ini

@@ -118,6 +118,8 @@ preview_limit = 25
 # Triplestore max rows limit
 result_set_max_rows = 10000
 
+single_tenant=False
+
 [federation]
 # Query engine can be corese or fedx
 query_engine = corese

tests/test_api.py

@@ -42,7 +42,8 @@ def test_start(self, client):
             "namespaceInternal": client.get_config('triplestore', 'namespace_internal'),
             "proxyPath": "/",
             "user": {},
-            "logged": False
+            "logged": False,
+            "singleTenant": False
         }
         response = client.client.get('/api/start')
         assert response.status_code == 200