Merge f59a08e into 8859bc1

askomics · Jan 26, 2022 · 8485d69 · 8485d69
2 parents 8859bc1 + f59a08e
commit 8485d69
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Showing 7 changed files with 50 additions and 41 deletions.
diff --git a/.github/workflows/lint_test.yml b/.github/workflows/lint_test.yml
@@ -50,7 +50,7 @@ jobs:
         docker pull xgaia/corese:latest
         docker pull xgaia/isql-api:2.1.1
         docker pull xgaia/simple-ldap:latest
-        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/$/ askomics-host/' >> /etc/hosts && /virtuoso/virtuoso.sh"
+        docker run -d --name virtuoso -p 8891:8890 -p 1112:1111 -e DBA_PASSWORD=dba -e DEFAULT_GRAPH=http://localhost:8891/DAV -t askomics/virtuoso:7.2.5.1 /bin/sh -c "netstat -nr | grep '^0\.0\.0\.0' | grep -oE '((1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])\.){3}(1?[0-9][0-9]?|2[0-4][0-9]|25[0-5])' | grep -v '^0\.0\.0\.0' | sed 's/$/ askomics-host/' >> /etc/hosts && /virtuoso/virtuoso.sh"
         sleep 1m
         docker run -d --name redis -p 6380:6379 -t redis:4.0
         docker run -d --name galaxy -p 8081:80 -t bgruening/galaxy-stable:20.05

diff --git a/askomics/libaskomics/SparqlQueryLauncher.py b/askomics/libaskomics/SparqlQueryLauncher.py
@@ -44,6 +44,7 @@ def __init__(self, app, session, get_result_query=False, federated=False, endpoi
         except Exception:
             pass
 
+        local = False
         # Use the federated query engine
         if federated:
             self.federated = True
@@ -65,16 +66,20 @@ def __init__(self, app, session, get_result_query=False, federated=False, endpoi
             self.triplestore = self.settings.get('triplestore', 'triplestore')
             self.url_endpoint = self.settings.get('triplestore', 'endpoint')
             self.url_updatepoint = self.settings.get('triplestore', 'updatepoint')
+            local = True
+
+        self.endpoint = SPARQLWrapper(self.url_endpoint, self.url_updatepoint)
+
+        if local:
             try:
                 self.endpoint.setCredentials(
                     self.settings.get('triplestore', 'username'),
                     self.settings.get('triplestore', 'password')
                 )
+                self.endpoint.setHTTPAuth(self.settings.get('triplestore', 'http_auth', fallback="basic"))
             except Exception:
                 pass
 
-        self.endpoint = SPARQLWrapper(self.url_endpoint, self.url_updatepoint)
-
     def load_data(self, file_name, graph, host_url):
         """Load data in function of the triplestore
 

diff --git a/askomics/react/src/routes/datasets/datasetstable.jsx b/askomics/react/src/routes/datasets/datasetstable.jsx
@@ -118,7 +118,7 @@ export default class DatasetsTable extends Component {
         return (
           <FormGroup>
             <div>
-              <CustomInput disabled={this.props.config.user.admin ? false : true} type="switch" id={row.id} onChange={this.togglePublicDataset} checked={cell} value={cell} />
+              <CustomInput disabled={this.props.config.user.admin === 1 ? false : true} type="switch" id={row.id} onChange={this.togglePublicDataset} checked={cell} value={cell} />
             </div>
           </FormGroup>
         )
@@ -209,4 +209,4 @@ DatasetsTable.propTypes = {
   waiting: PropTypes.bool,
   datasets: PropTypes.object,
   config: PropTypes.object
-}
+}
diff --git a/config/askomics.ini.template b/config/askomics.ini.template
@@ -12,9 +12,9 @@ debug = false
 debug_ttl = false
 
 # If Askomics is running under a sub path (like http://example.org/askomics, subpath is /askomics)
-#reverse_proxy_path = 
+#reverse_proxy_path =
 
-# subtitle = 
+# subtitle =
 footer_message = Welcome to AskOmics!
 #front_message=
 
@@ -61,12 +61,12 @@ instance_url = http://localhost:5000
 # If set, host, port and sender are mandatory.
 # user and password are optional
 # connection: starttls or nothing
-#smtp_host = 
-#smtp_port = 
-#smtp_sender = 
-#smtp_user = 
-#smtp_password = 
-#smtp_connection = 
+#smtp_host =
+#smtp_port =
+#smtp_sender =
+#smtp_user =
+#smtp_password =
+#smtp_connection =
 
 # LDAP
 ldap_auth = false
@@ -80,16 +80,16 @@ ldap_username_attribute = uid
 ldap_first_name_attribute = givenName
 ldap_surname_attribute = sn
 ldap_mail_attribute = mail
-#ldap_password_reset_link = 
-#ldap_account_link = 
+#ldap_password_reset_link =
+#ldap_account_link =
 
 [triplestore]
 # name of the triplestore, can be virtuoso or fuseki
 triplestore = virtuoso
 # Sparql endpoint
-endpoint = http://localhost:8890/sparql
+endpoint = http://localhost:8890/sparql-auth
 # Sparql updatepoint
-updatepoint = http://localhost:8890/sparql
+updatepoint = http://localhost:8890/sparql-auth
 # Isql API
 # If triplestore is virtuoso, set the (optional) isql api for fastest graph deletion
 #isqlapi = http://localhost:5050
@@ -98,8 +98,10 @@ updatepoint = http://localhost:8890/sparql
 # Triplestore credentials
 username = dba
 password = dba
+# Http auth method for sparqlwrapper: basic or digest (virtuoso require digest)
+http_auth = digest
 # If the triplesotre and askomics are on different network, the loadurl is askomics url accessible by the triplesotre
-# load_url = 
+# load_url =
 upload_method = load
 # Number of triple to integrate in one request
 chunk_size = 60000

diff --git a/config/askomics.test.ini b/config/askomics.test.ini
@@ -11,7 +11,7 @@ result_backend = redis://localhost:6380
 debug = false
 debug_ttl = false
 
-# subtitle = 
+# subtitle =
 footer_message = Test
 #front_message=
 
@@ -55,12 +55,12 @@ instance_url = http://localhost:5000
 # If set, host, port and sender are mandatory.
 # user and password are optional
 # connection: starttls or nothing
-#smtp_host = 
-#smtp_port = 
-#smtp_sender = 
-#smtp_user = 
-#smtp_password = 
-#smtp_connection = 
+#smtp_host =
+#smtp_port =
+#smtp_sender =
+#smtp_user =
+#smtp_password =
+#smtp_connection =
 
 # LDAP
 ldap_auth = false
@@ -74,16 +74,16 @@ ldap_username_attribute = uid
 ldap_first_name_attribute = givenName
 ldap_surname_attribute = sn
 ldap_mail_attribute = mail
-#ldap_password_reset_link = 
-#ldap_account_link = 
+#ldap_password_reset_link =
+#ldap_account_link =
 
 [triplestore]
 # name of the triplestore, can be virtuoso or fuseki
 triplestore = virtuoso
 # Sparql endpoint
-endpoint = http://localhost:8891/sparql
+endpoint = http://localhost:8891/sparql-auth
 # Sparql updatepoint
-updatepoint = http://localhost:8891/sparql
+updatepoint = http://localhost:8891/sparql-auth
 # Isql API
 # If triplestore is virtuoso, set the (optional) isql api for fastest graph deletion
 isqlapi = http://localhost:5051
@@ -92,8 +92,10 @@ isqlapi = http://localhost:5051
 # Triplestore credentials
 username = dba
 password = dba
-# If the triplesotre and askomics are on different network, the loadurl is askomics url accessible by the triplesotre
-# load_url = 
+# Http auth method for sparqlwrapper: basic or digest (virtuoso require digest)
+http_auth = digest
+# If the triplestore and askomics are on different network, the loadurl is askomics url accessible by the triplesotre
+# load_url =
 upload_method = insert
 # Number of triple to integrate in one request
 chunk_size = 60000

diff --git a/tests/results/abstraction.json b/tests/results/abstraction.json
@@ -561,7 +561,7 @@
     "entities": [
       {
         "endpoints": [
-          "http://localhost:8891/sparql"
+          "http://localhost:8891/sparql-auth"
         ],
         "faldo": true,
         "graphs": [
@@ -575,7 +575,7 @@
       },
       {
         "endpoints": [
-          "http://localhost:8891/sparql"
+          "http://localhost:8891/sparql-auth"
         ],
         "faldo": true,
         "graphs": [
@@ -589,7 +589,7 @@
       },
       {
         "endpoints": [
-          "http://localhost:8891/sparql"
+          "http://localhost:8891/sparql-auth"
         ],
         "faldo": true,
         "graphs": [
@@ -602,7 +602,7 @@
       },
       {
         "endpoints": [
-          "http://localhost:8891/sparql"
+          "http://localhost:8891/sparql-auth"
         ],
         "faldo": false,
         "graphs": [

diff --git a/tests/results/startpoints.json b/tests/results/startpoints.json
@@ -8,10 +8,10 @@
     [{
         "endpoints": [{
             "name": "local",
-            "url": "http://localhost:8891/sparql"
+            "url": "http://localhost:8891/sparql-auth"
         }, {
             "name": "local",
-            "url": "http://localhost:8891/sparql"
+            "url": "http://localhost:8891/sparql-auth"
         }],
         "entity":
         "http://askomics.org/test/data/transcript",
@@ -37,10 +37,10 @@
      {
          "endpoints": [{
              "name": "local",
-             "url": "http://localhost:8891/sparql"
+             "url": "http://localhost:8891/sparql-auth"
          }, {
              "name": "local",
-             "url": "http://localhost:8891/sparql"
+             "url": "http://localhost:8891/sparql-auth"
          }],
          "entity":
          "http://askomics.org/test/data/gene",
@@ -70,7 +70,7 @@
      {
          "endpoints": [{
              "name": "local",
-             "url": "http://localhost:8891/sparql"
+             "url": "http://localhost:8891/sparql-auth"
          }],
          "entity":
          "http://askomics.org/test/data/DifferentialExpression",
@@ -89,7 +89,7 @@
      {
          "endpoints": [{
              "name": "local",
-             "url": "http://localhost:8891/sparql"
+             "url": "http://localhost:8891/sparql-auth"
          }],
          "entity":
          "http://askomics.org/test/data/QTL",