fixes for ebi k8s deployment

EBISPOT · Aug 19, 2024 · e1e1e9c · e1e1e9c
1 parent aa79943
commit e1e1e9c
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Showing 11 changed files with 32 additions and 18 deletions.
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -39,6 +39,13 @@ jobs:
           docker tag ghcr.io/ebispot/grebi_resolver_service:${{github.sha}} ghcr.io/ebispot/grebi_resolver_service:${{ github.ref_name }}
           docker push --all-tags ghcr.io/ebispot/grebi_resolver_service
 
+      - name: Build and push GrEBI summary service Docker image
+        run: |
+          cd grebi_summary_service
+          docker build -t ghcr.io/ebispot/grebi_summary_service:${{ github.sha }} .
+          docker tag ghcr.io/ebispot/grebi_summary_service:${{github.sha}} ghcr.io/ebispot/grebi_summary_service:${{ github.ref_name }}
+          docker push --all-tags ghcr.io/ebispot/grebi_summary_service
+
       - name: Build and push GrEBI UI Docker image
         run: |
           cd grebi_ui

diff --git a/grebi_resolver_service/Dockerfile b/grebi_resolver_service/Dockerfile
@@ -1,6 +1,7 @@
 
-FROM maven:3.9.6-amazoncorretto-17
+FROM maven:3.9-eclipse-temurin-11
 
+RUN mkdir -p /opt
 COPY . /opt/
 RUN cd /opt/ && ls && mvn clean package assembly:single -DskipTests
 

diff --git a/grebi_resolver_service/pom.xml b/grebi_resolver_service/pom.xml
@@ -15,8 +15,8 @@
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <maven.compiler.source>17</maven.compiler.source>
-    <maven.compiler.target>17</maven.compiler.target>
+    <maven.compiler.source>11</maven.compiler.source>
+    <maven.compiler.target>11</maven.compiler.target>
   </properties>
 
   <dependencies>

diff --git a/grebi_resolver_service/src/main/java/uk/ac/ebi/grebi_resolver_service/GrebiResolverSvc.java b/grebi_resolver_service/src/main/java/uk/ac/ebi/grebi_resolver_service/GrebiResolverSvc.java
@@ -45,7 +45,7 @@ public static void main(String[] args) {
         }
 
         Javalin app = Javalin.create(config -> {
-        }).start(8080);
+        }).start("0.0.0.0", 8080);
 
         app.get("/subgraphs", ctx -> {
             ctx.contentType("application/json");

diff --git a/grebi_summary_service/src/main/java/uk/ac/ebi/grebi_summary_service/GrebiSummarySvc.java b/grebi_summary_service/src/main/java/uk/ac/ebi/grebi_summary_service/GrebiSummarySvc.java
@@ -29,7 +29,7 @@ public static void main(String[] args) throws FileNotFoundException {
         }
 
         Javalin app = Javalin.create(config -> {
-        }).start(8081);
+        }).start("0.0.0.0", 8081);
 
         app.get("/", ctx -> {
             ctx.contentType("application/json");

diff --git a/k8chart/templates/grebi-backend-deployment.yaml b/k8chart/templates/grebi-backend-deployment.yaml
@@ -19,7 +19,7 @@ spec:
           image: ghcr.io/ebispot/grebi_api:{{.Values.imageTag}}
           imagePullPolicy: Always
           ports:
-            - containerPort: 8080
+            - containerPort: 8090
           resources:
             requests:
               memory: 8Gi
@@ -32,6 +32,10 @@ spec:
               value: http://{{ .Release.Name }}-solr:8983
             - name: GREBI_NEO4J_HOST
               value: bolt://{{ .Release.Name }}-neo4j:7687
+            - name: GREBI_RESOLVER_HOST
+              value: http://{{ .Release.Name }}-resolver:8080
+            - name: GREBI_SUMMARY_HOST
+              value: http://{{ .Release.Name }}-summary-service:8081
             - name: GREBI_CONTEXT_PATH
               value: /kg
             - name: JDK_JAVA_OPTIONS

diff --git a/k8chart/templates/grebi-backend-service.yaml b/k8chart/templates/grebi-backend-service.yaml
@@ -8,6 +8,6 @@ spec:
   type: NodePort
   ports:
   - name: "application"
-    port: 8080
+    port: 8090
   selector:
     app: {{ .Release.Name }}-backend
diff --git a/k8chart/templates/grebi-neo4j-deployment.yaml b/k8chart/templates/grebi-neo4j-deployment.yaml
@@ -30,20 +30,20 @@ spec:
               name: {{ .Release.Name }}-neo4j-storage
           resources:
             requests:
-              memory: 40Gi
+              memory: 30Gi
               cpu: 4
             limits:
-              memory: 40Gi
+              memory: 30Gi
               cpu: 4
           env:
             - name: NEO4J_AUTH
               value: none
             - name: NEO4J_server_memory_heap_initial__size
-              value: 15000m
+              value: 12000m
             - name: NEO4J_server_memory_heap_max__size
-              value: 15000m
+              value: 12000m
             - name: NEO4J_server_memory_pagecache_size
-              value: 15g
+              value: 12g
             - name: NEO4J_PLUGINS
               value: \["apoc"\]
           ports:

diff --git a/k8chart/templates/grebi-resolver-deployment.yaml b/k8chart/templates/grebi-resolver-deployment.yaml
@@ -21,15 +21,16 @@ spec:
       containers:
         - name: resolver
           image: ghcr.io/ebispot/grebi_resolver_service:{{.Values.imageTag}}
+          imagePullPolicy: Always
           volumeMounts:
             - mountPath: "/data"
               name: {{ .Release.Name }}-resolver-storage
           resources:
             requests:
-              memory: 8Gi
+              memory: 16Gi
               cpu: 2
             limits:
-              memory: 8Gi
+              memory: 16Gi
               cpu: 2
           env:
             - name: GREBI_ROCKSDB_SEARCH_PATH

diff --git a/k8chart/templates/grebi-summary-service-deployment.yaml b/k8chart/templates/grebi-summary-service-deployment.yaml
@@ -21,16 +21,17 @@ spec:
       containers:
         - name: summary-service
           image: ghcr.io/ebispot/grebi_summary_service:{{.Values.imageTag}}
+          imagePullPolicy: Always
           volumeMounts:
             - mountPath: "/data"
               name: {{ .Release.Name }}-summary-service-storage
           resources:
             requests:
               memory: 2Gi
-              cpu: 2
+              cpu: 0.5
             limits:
               memory: 2Gi
-              cpu: 2
+              cpu: 0.5
           env:
             - name: GREBI_SUMMARY_JSON_SEARCH_PATH
               value: /data

diff --git a/k8chart/templates/grebi-summary-service.yaml b/k8chart/templates/grebi-summary-service.yaml
@@ -6,8 +6,8 @@ metadata:
     app: {{ .Release.Name }}-summary-service
 spec:
   ports:
-      - port: 8080
-        targetPort: 8080
+      - port: 8081
+        targetPort: 8081
         name: http
         protocol: TCP
   selector: