Merge branch 'main' into feature/2696-Document-level-recommendations

* main:
  No issue. Added another example for the MTAS search
  #4388 - Mention health checking endpoint in admin guide
  #4386 - User "null" sometimes shows up in recent activity
  #916 - Changing URL of remote KB requires server restart

inception/inception-api-annotation/src/main/resources/META-INF/asciidoc/admin-guide/settings_segmentation.adoc

@@ -24,7 +24,7 @@ adding/removing/changing segmentation annotations (i.e. sentences or tokens).
 
 This section describes the global settings related to the support for editable segmentation annotations (i.e. sentences or tokens).
 
-.Knowledge base settings overview
+.Segmentation settings overview
 [cols="4*", options="header"]
 |===
 | Setting
@@ -33,8 +33,8 @@ This section describes the global settings related to the support for editable s
 | Example
 
 
-| ui.sentence-layer-editable=true
+| `ui.sentence-layer-editable`
 | Enable/disable editing sentences
-| false
-| true
+| `false`
+| `true`
 |===

inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/metrics_monitoring.adoc

@@ -14,9 +14,50 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
+[[sect_monitoring]]
 = Monitoring
 
-== Available metrics
+[[sect_health_check]]
+== Health check
+
+{product-name} offers a health-checking endpoint at `.../actuator/health`. It provides a JSON response indicating
+whether the application is up and running.
+
+[source,json]
+----
+{
+   "status":"UP",
+   "components":{
+      "db":{
+         "status":"UP",
+         "details":{
+            "database":"MariaDB",
+            "validationQuery":"isValid()"
+         }
+      },
+      "diskSpace":{
+         "status":"UP",
+         "details":{
+            "total": ...,
+            "free": ...,
+            "threshold": ...,
+            "exists":true
+         }
+      },
+      "ping":{
+         "status":"UP"
+      }
+   }
+}
+----
+
+
+== Metrics
+
+====
+NOTE: to make the metrics available `spring.jmx.enabled=true` and `monitoring.metrics.enabled=true`  must be set in 
+       the `settings.properties` file  (see <<sect_home_folder>> on this file)..
+====
 
 We expose some metrics of the running {product-name} instance via JMX. These are currently
 
@@ -25,10 +66,6 @@ We expose some metrics of the running {product-name} instance via JMX. These are
 * the number of enabled recommenders
 * the number of annotation documents i.e. documents being annotated per user
 
-To make the metrics available `spring.jmx.enabled=true`
-and `monitoring.metrics.enabled=true` 
-must be set in the `settings.properties` file 
-(see <<sect_home_folder>> on this file).
 
 == Setting up metrics exporter
 
@@ -40,7 +77,8 @@ file next to the {product-name} .jar file. An example `config.yml` file that exp
 INCEpTION but not webanno brat metrics (metrics associated with brat rendering) and conforms JMX metric 
 names to https://prometheus.io/docs/practices/naming/[Prometheus Naming conventions] is:
 
-....
+[source,yaml]
+----
 ssl: false
 whitelistObjectNames: ["de.tudarmstadt.ukp.inception.recommendation.metrics:*", 
 "de.tudarmstadt.ukp.clarin.webanno.api.dao.metrics:*", "de.tudarmstadt.ukp.clarin.webanno.security.metrics:*"]
@@ -61,16 +99,17 @@ rules:
     help: "Inception metric $4"
     type: GAUGE
     attrNameSnakeCase: true
-....
+----
 
 The following line will run the JMX exporter for the JVM that runs the inception.jar. 
 The exporter will expose the metrics on the http-endpoint _localhost:9404_.
 Make sure to use a port, 9404 in this case, that is not open to the public 
 (only to the local network that your Prometheus instance runs in).
 
-....
-java -javaagent:./jmx_prometheus_javaagent-0.13.0.jar=9404:config.yaml -jar inception.jar
-....
+[source,sh]
+----
+$ java -javaagent:./jmx_prometheus_javaagent-0.13.0.jar=9404:config.yaml -jar inception.jar
+----
 
 The JMX exporter will also automatically expose JVM metrics in the `java.lang` namespace 
 which can be used to e.g. monitor memory usage:
@@ -117,6 +156,7 @@ By default, only unhandled exceptions are sent to Sentry. This behavior can be t
 
 More option that can be overwritten are listed in https://docs.sentry.io/platforms/java/guides/spring-boot/configuration/[the official Sentry SDK ducumentation].
 
+
 == Scheduling
 The default schedule for pulling of Prometheus is 10s, however it is necessary to make this a longer 
 interval to avoid overwhelming your {product-name} instance with requests for metrics. 

inception/inception-kb/src/main/java/de/tudarmstadt/ukp/inception/kb/KnowledgeBaseServiceImpl.java

@@ -47,6 +47,7 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
@@ -80,6 +81,7 @@
 import org.eclipse.rdf4j.repository.sail.SailRepository;
 import org.eclipse.rdf4j.repository.sail.SailRepositoryConnection;
 import org.eclipse.rdf4j.repository.sail.config.SailRepositoryConfig;
+import org.eclipse.rdf4j.repository.sparql.SPARQLConnection;
 import org.eclipse.rdf4j.repository.sparql.SPARQLRepository;
 import org.eclipse.rdf4j.repository.sparql.config.SPARQLRepositoryConfig;
 import org.eclipse.rdf4j.rio.RDFFormat;
@@ -323,7 +325,7 @@ public void registerKnowledgeBase(KnowledgeBase aKB, RepositoryImplConfig aCfg)
 
         // We want to have a separate Lucene index for every local repo, so we need to hack the
         // index dir in here because this is the place where we finally know the repo ID.
-        syncIndexParameters(aKB, aCfg);
+        setLuceneIndexConfigurtionParameters(aKB, aCfg);
 
         repoManager.addRepositoryConfig(new RepositoryConfig(repositoryId, aCfg));
         entityManager.persist(aKB);
@@ -407,12 +409,17 @@ public void updateKnowledgeBase(KnowledgeBase kb)
 
     @Transactional
     @Override
-    public void updateKnowledgeBase(KnowledgeBase kb, RepositoryImplConfig cfg)
+    public void updateKnowledgeBase(KnowledgeBase aKB, RepositoryImplConfig cfg)
         throws RepositoryException, RepositoryConfigException
     {
-        assertRegistration(kb);
-        repoManager.addRepositoryConfig(new RepositoryConfig(kb.getRepositoryId(), cfg));
-        updateKnowledgeBase(kb);
+        assertRegistration(aKB);
+        repoManager.addRepositoryConfig(new RepositoryConfig(aKB.getRepositoryId(), cfg));
+
+        // Drop cached results from the KB being updated
+        queryCache.asMap().keySet()
+                .removeIf(key -> Objects.equals(key.kb.getRepositoryId(), aKB.getRepositoryId()));
+
+        updateKnowledgeBase(aKB);
     }
 
     @Transactional
@@ -517,7 +524,9 @@ public RepositoryConnection getConnection(KnowledgeBase kb)
             {
                 skipCertificateChecks(kb.isSkipSslValidation());
 
-                syncIndexParameters(kb, getDelegate());
+                syncLuceneQueryLiveParameters(kb, getDelegate());
+
+                syncSparqlUrlLiveParameters(kb, getDelegate());
             }
 
             @Override
@@ -1393,11 +1402,11 @@ void reconfigureLocalKnowledgeBase(KnowledgeBase aKB)
          */
 
         var config = getNativeConfig();
-        syncIndexParameters(aKB, config);
+        setLuceneIndexConfigurtionParameters(aKB, config);
         repoManager.addRepositoryConfig(new RepositoryConfig(aKB.getRepositoryId(), config));
     }
 
-    private void syncIndexParameters(KnowledgeBase aKB, RepositoryImplConfig aCfg)
+    private void setLuceneIndexConfigurtionParameters(KnowledgeBase aKB, RepositoryImplConfig aCfg)
     {
         assertRegistration(aKB);
 
@@ -1421,7 +1430,7 @@ private void syncIndexParameters(KnowledgeBase aKB, RepositoryImplConfig aCfg)
         }
     }
 
-    private void syncIndexParameters(KnowledgeBase kb, RepositoryConnection aConn)
+    private void syncLuceneQueryLiveParameters(KnowledgeBase kb, RepositoryConnection aConn)
     {
         try {
             if (aConn instanceof SailRepositoryConnection sailRepo) {
@@ -1440,6 +1449,35 @@ private void syncIndexParameters(KnowledgeBase kb, RepositoryConnection aConn)
         }
     }
 
+    private void syncSparqlUrlLiveParameters(KnowledgeBase kb,
+            RepositoryConnection aRepositoryConnection)
+    {
+        try {
+            if (aRepositoryConnection instanceof SPARQLConnection sparqlConnection) {
+                var sparqlRepoConfig = (SPARQLRepositoryConfig) getKnowledgeBaseConfig(kb);
+                var repository = sparqlConnection.getRepository();
+
+                var queryEndpointUrl = sparqlRepoConfig.getQueryEndpointUrl();
+                var updateEndpointUrl = sparqlRepoConfig.getUpdateEndpointUrl();
+                if (updateEndpointUrl == null) {
+                    updateEndpointUrl = queryEndpointUrl;
+                }
+
+                writeField(repository, "queryEndpointUrl", queryEndpointUrl, true);
+                writeField(repository, "updateEndpointUrl", updateEndpointUrl, true);
+
+                var session = readField(sparqlConnection, "client", true);
+                writeField(session, "queryURL", queryEndpointUrl, true);
+                writeField(session, "updateURL", updateEndpointUrl, true);
+            }
+        }
+        catch (Exception e) {
+            throw new RuntimeException("Unable to sync URL into live SPARQL connection - "
+                    + "maybe the SPARQLConnection or SPARQLProtocolSession implementation has changed.",
+                    e);
+        }
+    }
+
     @Override
     public void rebuildFullTextIndex(KnowledgeBase aKB) throws Exception
     {

inception/inception-search-mtas/src/main/resources/META-INF/asciidoc/user-guide/search-mtas.adoc

@@ -38,7 +38,8 @@ feature has the given value.
 Notice that the multi-token query syntax can also be used to retrieve single token annotations (e.g.
 POS or lemma annotations).
 
-=== Basic Annotation queries
+
+=== Text queriess
 
 .Single token: all occurrences of the token *Galicia*
 ----
@@ -59,6 +60,9 @@ The capital of Galicia
 ----
 "The" "capital" "of" "Galicia"
 ----
+
+
+=== Span layer queries
 
 .Lemma: all occurrences of the lemma *sign*
 ----
@@ -168,6 +172,12 @@ The capital of Galicia
 (<Named_entity.value="OTH"/> | <Named_entity.value="LOC"/>) intersecting <SemArg/>
 ----
 
+.Search for sentences containing a PER named entity
+----
+<s> []{0,50} <Named_entity.value="PER"/> []{0,50} </s> within <s/>
+----
+
+
 === Relation layer queries
 
 {product-name} allows queries over relation annotations as well. When relations are indexed, they