Merge pull request #262 from ofilangi/federation

Fix somes bugs with owl integration

askomics/ask_view.py

@@ -305,16 +305,22 @@ def delete_endpoints(self):
         """
 
         """
+        self.data = {}
 
         self.checkAuthSession()
 
-        if 'endpoints' not in self.request.json_body:
-            raise exc.exception_response(404)
+        if 'id_endpoints' not in self.request.json_body:
+            self.data['error'] = 'Devel : id_endpoints value is not defined !'
+            self.request.response.status = 400
+            return self.data
+
+        endpoints = self.request.json_body['id_endpoints']
 
         em = EndpointManager(self.settings, self.request.session)
 
-        for id in self.request.json_body['endpoints']:
-            em.remove(id)
+        for url in endpoints:
+            em.remove(url)
+        ##raise ValueError("ok")
 
     @view_config(route_name='add_endpoint', request_method='POST')
     def add_endpoint(self):
@@ -415,12 +421,16 @@ def list_endpoints(self):
         """
 
         session = {}
+        try:
+            em = EndpointManager(self.settings, self.request.session)
+            session['askomics'] = em.listEndpoints()
 
-        em = EndpointManager(self.settings, self.request.session)
-        session['askomics'] = em.listEndpoints()
+            sqb = SparqlQueryBuilder(self.settings, self.request.session)
+            session['external'] = sqb.getExternalServiceEndpoint()
+        except Exception as e:
+            traceback.print_exc(file=sys.stdout)
+            self.data['error'] = str(e)
 
-        sqb = SparqlQueryBuilder(self.settings, self.request.session)
-        session['external'] = sqb.getExternalServiceEndpoint()
         return session
 
 

askomics/libaskomics/EndpointManager.py

@@ -67,29 +67,43 @@ def saveEndpoint(self,name,url,auth,isenable):
         conn.close()
         return ID
 
-    def enable(self,name):
+    def enable(self,id):
 
         conn = sqlite3.connect(self.pathdb,uri=True)
         c = conn.cursor()
 
         reqSql = "UPDATE endpoints SET "\
                 + " enable = 1 ," \
                 + " message = '' " \
-                + " WHERE name = '"+str(name)+"'"
+                + " WHERE id = '"+str(id)+"'"
 
         c.execute(reqSql)
         conn.commit()
         conn.close()
 
-    def disable(self,name,message):
+    def disable(self,id,message):
 
         conn = sqlite3.connect(self.pathdb,uri=True)
         c = conn.cursor()
 
         reqSql = "UPDATE endpoints SET "\
                 + " enable = 0 , " \
                 + " message = '"+message+"' " \
-                + " WHERE name = '"+str(name)+"'"
+                + " WHERE id = '"+str(id)+"'"
+
+        c.execute(reqSql)
+        conn.commit()
+        conn.close()
+
+    def disableUrl(self,endp,message):
+
+        conn = sqlite3.connect(self.pathdb,uri=True)
+        c = conn.cursor()
+
+        reqSql = "UPDATE endpoints SET "\
+                + " enable = 0 , " \
+                + " message = '"+message+"' " \
+                + " WHERE url = '"+str(endp)+"'"
 
         c.execute(reqSql)
         conn.commit()
@@ -168,18 +182,19 @@ def listActiveEndpoints(self):
 
         return data
 
-    def remove(self,name):
-
+    def remove(self,id):
+        print("================================ REMOVE FROM DATABASE ENDPOINT :"+str(id))
         conn = sqlite3.connect(self.pathdb,uri=True)
         c = conn.cursor()
 
-        reqSql = "DELETE FROM endpoints WHERE name = '"+ str(name)+"'"
-
+        reqSql = "DELETE FROM endpoints WHERE id = '"+ str(id)+"'"
+        print(reqSql)
         try:
             c.execute(reqSql)
             conn.commit()
         except sqlite3.OperationalError as e :
             self.log.warn("Jobs database does not exist .")
+            print(e)
 
         conn.close()
 

askomics/libaskomics/TripleStoreExplorer.py

@@ -45,7 +45,7 @@ def get_start_points(self):
         ql = MultipleQueryLauncher(self.settings, self.session)
         em = EndpointManager(self.settings, self.session)
 
-        lEndp = em.listEndpoints()
+        lEndp = em.listActiveEndpoints()
         results = ql.process_query(sqg.get_public_start_point().query,lEndp,indexByEndpoint=True)
         r2 = ql.process_query(sqg.get_user_start_point().query,lEndp,indexByEndpoint=True)
 
@@ -85,7 +85,7 @@ def getUserAbstraction(self):
         sqg = SparqlQueryGraph(self.settings, self.session)
         ql = MultipleQueryLauncher(self.settings, self.session)
         em = EndpointManager(self.settings, self.session)
-        lEndp = em.listEndpoints()
+        lEndp = em.listActiveEndpoints()
 
         data['relations'] = ql.process_query(sqg.get_public_abstraction_relation('owl:ObjectProperty').query,lEndp)
         data['relations'] += ql.process_query(sqg.get_user_abstraction_relation('owl:ObjectProperty').query,lEndp)
@@ -207,7 +207,7 @@ def get_prefix_uri(self):
         sqg = SparqlQueryGraph(self.settings, self.session)
         ql = MultipleQueryLauncher(self.settings, self.session)
         em = EndpointManager(self.settings, self.session)
-        rs = ql.process_query(sqg.get_prefix_uri().query,em.listEndpoints())
+        rs = ql.process_query(sqg.get_prefix_uri().query,em.listActiveEndpoints())
         results = {}
         r_buf = {}
 

askomics/libaskomics/rdfdb/QueryLauncher.py

@@ -10,6 +10,7 @@
 import urllib.request
 
 from askomics.libaskomics.ParamManager import ParamManager
+from askomics.libaskomics.EndpointManager import EndpointManager
 
 class SPARQLError(RuntimeError):
     """
@@ -170,7 +171,10 @@ def _execute_query(self, query, log_raw_results=True, externalService=None):
             try:
                 results = data_endpoint.query().convert()
                 if type(results) != dict :
-                     raise ValueError("JSON is not supported by the sparql endpoint. Askomics can not support this format results :"+type(results).__module__+"."+type(results).__name__)
+                    error = "JSON is not supported by the sparql endpoint. Askomics can not support this format results :"+type(results).__module__+"."+type(results).__name__
+                    em = EndpointManager(self.settings, self.session)
+                    em.disableUrl(self.endpoint,error)
+                    results = []
 
             except urllib.error.URLError as URLError:
                 #url error, we disable the endpoint

askomics/libaskomics/source_file/SourceFileTsv.py

@@ -424,7 +424,7 @@ def get_domain_knowledge(self):
             ttl += (" , \n" + indent ).join(map(lambda category : self.encode_to_rdf_uri(category,prefix="askomics:"), categories)) + " .\n"
             for item in categories:
                 if item.strip() != "":
-                    ttl += self.encode_to_rdf_uri(item,prefix="askomics:") + " rdf:type " + self.encode_to_rdf_uri(header,prefix="askomics:") + " ;\n" + len(item) * " " + "  rdfs:label " + self.escape['text'](item,'') + "^^xsd:string .\n"
+                    ttl += self.encode_to_rdf_uri(item,prefix="askomics:") + " rdf:type " + self.encode_to_rdf_uri(header+"CategoryValue",prefix="askomics:") + " ;\n" + len(item) * " " + "  rdfs:label " + self.escape['text'](item,'') + "^^xsd:string .\n"
 
         return ttl
 

askomics/libaskomics/source_file/SourceFileTtl.py

@@ -22,7 +22,11 @@ class SourceFileTtl(SourceFile):
 
     def __init__(self, settings, session, path, file_type='ttl'):
 
-        newfile = self.convert_to_ttl(path,file_type)
+        newfile = path
+
+        if not file_type == 'ttl':
+            newfile = self.convert_to_ttl(path,file_type)
+
         SourceFile.__init__(self, settings, session, newfile)
 
         self.type = 'ttl'

askomics/static/src/js/core/IHMLocal.js

@@ -423,13 +423,13 @@ class IHMLocal {
                   if ($(this).is(':checked')) {selected.push($(this).attr('name'));}
               });
               let service = new RestServiceJs('delete_endpoints');
-              let model = {'endpoints': selected};
+              let model = {'id_endpoints': selected};
               //show the spinner
               $('#spinner_delete').removeClass('hidden');
               service.post(model, function(data) {
                   __ihm.loadEndpoints();
-                  __ihm.stopSession();
-                  __ihm.resetStats();
+                  //__ihm.stopSession();
+                  //__ihm.resetStats();
               });
           });
 
@@ -820,13 +820,14 @@ class IHMLocal {
         new AskomicsJobsViewManager().loadjob().then(function () {
           new AskomicsJobsViewManager().update_jobview ();
         });
-        __ihm.displayModal('Loading data...', '', 'Close');
       });
+
+      __ihm.displayModal('Loading data...', '', 'Close');
     }
 
     load_remote_data(public_d) {
       let url = $('#data-url').val();
-      load_remote_data_onclick(public_d,url);
+      __ihm.load_remote_data_onclick(public_d,url);
     }
 
     set_upload_url() {

askomics/static/src/templates/handlebars/galaxy_datasets.hbs

@@ -49,5 +49,5 @@
     </tbody>
 </table>
 
-<button id="upload_galaxy" type="button" class="btn btn-default" disabled><i class="fa fa-cloud-upload text-primary"></i> Upload to AskOmics</button>
+<button id="upload_galaxy" type="button" class="btn btn-default"><i class="fa fa-cloud-upload text-primary"></i> Upload to AskOmics</button>
 <i class="hidden fa fa-spinner pulse" id='spinner_galaxy-upload'></i>

askomics/test/EndpointManager_test.py

@@ -52,7 +52,7 @@ def test_disable_enable(self):
         listActiveEndp = jm.listActiveEndpoints()
         assert len(listActiveEndp) == 0
 
-        jm.enable("testNameEndpoint")
+        jm.enable(1)
         listActiveEndp = jm.listActiveEndpoints()
 
         assert len(listActiveEndp) == 1
@@ -61,7 +61,7 @@ def test_disable_enable(self):
                 and listActiveEndp[0]['endpoint'] == "http://www.urlTPS.com"
                 and listActiveEndp[0]['auth'].lower() == "digest")
 
-        jm.disable("testNameEndpoint","test disable")
+        jm.disable(1,"test disable")
 
         listActiveEndp = jm.listActiveEndpoints()
 
@@ -83,10 +83,17 @@ def test_listEndpoints(self):
         listEndp = jm.listEndpoints()
         assert len(listEndp) == 1
         jm.remove("bidon")
-        jm.remove("testNameEndpoint")
+        jm.remove("1")
         listEndp = jm.listEndpoints()
         assert len(listEndp) == 0
 
+    def test_disableUrl(self):
+        jm = EndpointManager(self.settings, self.request.session)
+        jm.disableUrl("bidon","bidon")
+        jm.saveEndpoint("testNameEndpoint","http://www.urlTPS.com",'Digest',True)
+        jm.disableUrl("testNameEndpoint","bidon")
+        jm.remove("1")
+
     def test_raise_SQLException(self):
         jm = EndpointManager(self.settings, self.request.session)
         jm.drop()