Merge branch 'dev' into stable

EBISPOT · Jul 23, 2024 · 29ded3d · 29ded3d
2 parents bfb8201 + 89bdeec
commit 29ded3d
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diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/HealthCheckController.java b/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v2/HealthCheckController.java
@@ -0,0 +1,72 @@
+package uk.ac.ebi.spot.ols.controller.api.v2;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Pageable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+import org.springframework.http.ResponseEntity;
+import org.springframework.http.HttpStatus;
+import uk.ac.ebi.spot.ols.controller.api.v2.responses.V2PagedAndFacetedResponse;
+import uk.ac.ebi.spot.ols.model.v2.V2Entity;
+import uk.ac.ebi.spot.ols.repository.neo4j.OlsNeo4jClient;
+import uk.ac.ebi.spot.ols.repository.v2.V2OntologyRepository;
+
+import java.util.Map;
+
+@RestController
+@RequestMapping("/api/v2")
+public class HealthCheckController {
+    @Autowired
+    V2OntologyRepository ontologyRepository;
+
+    @Autowired
+    OlsNeo4jClient neo4jClient;
+    private static final Logger logger = LoggerFactory.getLogger(HealthCheckController.class);
+
+    @RequestMapping("/health")
+    public ResponseEntity<String> checkHealth() {
+        if (!checkSolr()) {
+            return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).body("Solr is not initialized.");
+        }
+        if (!checkNeo4j()) {
+            return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).body("Neo4j is not initialized.");
+        }
+        return ResponseEntity.ok("All systems are operational.");
+    }
+
+    private boolean checkNeo4j() {
+        try {
+            if (neo4jClient.getDatabaseNodeCount() > 0) {
+                logger.info("Neo4J is initialized.");
+                return true;
+            } else {
+                logger.error("Neo4J is not initialized yet as Neo4J node elements were less than 1.");
+                return false;
+            }
+        } catch (Exception e) {
+            logger.error("Neo4j endpoint returned an error.", e);
+            return false;
+        }
+    }
+
+    private boolean checkSolr() {
+        Pageable pageable = Pageable.ofSize(20);
+        try {
+            V2PagedAndFacetedResponse<V2Entity> result = new V2PagedAndFacetedResponse<>(
+                    ontologyRepository.find(pageable, "en", null, null, null,
+                            false, Map.of()));
+            if (result.totalElements > 0) {
+                logger.info("Solr is initialized.");
+                return true;
+            } else {
+                logger.error("Solr is not initialized yet as 'totalElements' in jsonResponse not found or less than 1.");
+                return false;
+            }
+        } catch (Exception e) {
+            logger.error("Solr health check returned an error.", e);
+            return false;
+        }
+    }
+}
diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/repository/neo4j/OlsNeo4jClient.java b/backend/src/main/java/uk/ac/ebi/spot/ols/repository/neo4j/OlsNeo4jClient.java
@@ -21,8 +21,13 @@ public class OlsNeo4jClient {
 
 	@Autowired
 	Neo4jClient neo4jClient;
-
+  
 	private static final Logger logger = LoggerFactory.getLogger(OlsNeo4jClient.class);
+
+
+	public long getDatabaseNodeCount() {
+		return neo4jClient.returnNodeCount();
+	}
 
     public Page<JsonElement> getAll(String type, Map<String,String> properties, Pageable pageable) {
 

diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/service/Neo4jClient.java b/backend/src/main/java/uk/ac/ebi/spot/ols/service/Neo4jClient.java
@@ -53,6 +53,13 @@ public Session getSession() {
 
 	}
 
+	public long returnNodeCount() {
+		Session session = getSession();
+		Result result = session.run("MATCH (n) RETURN COUNT(n)");
+		long count = result.single().get(0).asLong();
+		session.close();
+		return count;
+	}
 
 	// only used by OLS3 graph repo, remove at some point
 	public List<Map<String,Object>> rawQuery(String query) {

diff --git a/k8chart-dev/ols4/templates/ols4-backend-deployment.yaml b/k8chart-dev/ols4/templates/ols4-backend-deployment.yaml
@@ -29,6 +29,17 @@ spec:
           imagePullPolicy: Always
           ports:
             - containerPort: 8080
+          readinessProbe:
+            httpGet:
+              path: /ols4/api/v2/health  # Ensure this matches the context path
+              port: 8080
+              scheme: HTTP
+              httpHeaders:
+                - name: Host
+                  value: {{ .Release.Name }}-backend
+            initialDelaySeconds: 15
+            periodSeconds: 60
+            timeoutSeconds: 10
           resources:
             requests:
               memory: 10Gi

diff --git a/k8chart-dev/ols4/templates/ols4-frontend-deployment.yaml b/k8chart-dev/ols4/templates/ols4-frontend-deployment.yaml
@@ -23,6 +23,10 @@ spec:
                   operator: In
                   values:
                     - hh-rke-wp-webadmin-56-worker-2.caas.ebi.ac.uk
+      initContainers:
+        - name: wait-for-backend
+          image: busybox
+          command: [ 'sh', '-c', 'until nc -z {{ .Release.Name }}-backend 8080; do echo waiting for backend; sleep 5; done;' ]
       containers:
         - name: web
           image: ghcr.io/ebispot/ols4-frontend:{{.Values.imageTag}}

diff --git a/k8chart/ols4/templates/ols4-backend-deployment.yaml b/k8chart/ols4/templates/ols4-backend-deployment.yaml
@@ -30,6 +30,17 @@ spec:
           imagePullPolicy: Always
           ports:
             - containerPort: 8080
+          readinessProbe:
+            httpGet:
+              path: /ols4/api/v2/health
+              port: 8080
+              scheme: HTTP
+              httpHeaders:
+                - name: Host
+                  value: { { .Release.Name } }-backend
+            initialDelaySeconds: 15
+            periodSeconds: 60
+            timeoutSeconds: 10
           resources:
             requests:
               memory: 10Gi

diff --git a/k8chart/ols4/templates/ols4-frontend-deployment.yaml b/k8chart/ols4/templates/ols4-frontend-deployment.yaml
@@ -24,6 +24,10 @@ spec:
                   values:
                     - hh-rke-wp-webadmin-47-worker-4.caas.ebi.ac.uk
                     - hx-rke-wp-webadmin-40-worker-4.caas.ebi.ac.uk
+      initContainers:
+        - name: wait-for-backend
+          image: busybox
+          command: [ 'sh', '-c', 'until nc -z {{ .Release.Name }}-backend 8080; do echo waiting for backend; sleep 5; done;' ]
       containers:
         - name: web
           image: ghcr.io/ebispot/ols4-frontend:{{.Values.imageTag}}