Complex-Portal · jmedinaebi · Feb 27, 2026
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,136 @@
+image: docker:latest
+services:
+  - docker:stable-dind
+variables:
+  DOCKER_TLS_CERTDIR: ""
+stages:
+  - tests
+  - build-jar
+  - build-docker-image
+  - kubernetes-deploy
+
+unit-tests:
+  image: maven:3.6-jdk-11
+  stage: tests
+  script:
+    - mvn test -B -s settings.xml -P complex-ws,unit-tests
+  when: manual
+
+.maven-build:
+  needs: [ unit-tests ]
+  image: maven:3.6-jdk-11
+  stage: build-jar
+  script:
+    - mvn clean package -B -s settings.xml -P $MAVEN_PROFILES -Dmaven.test.skip=true
+    - POM_VERSION=$(mvn -Dexec.executable='echo' -Dexec.args='${project.version}' --non-recursive exec:exec -q)
+    - echo "IMAGE_TAG=$POM_VERSION-$PROFILE_SUFFIX-$CI_COMMIT_SHORT_SHA" > build.env
+  artifacts:
+    paths:
+      - target/*.war
+    reports:
+      dotenv: build.env
+  when: manual
+
+maven-build-test:
+  extends: .maven-build
+  variables:
+    MAVEN_PROFILES: "complex-ws,k8s-solr,test"
+    PROFILE_SUFFIX: "test"
+
+maven-build-prod-hx:
+  extends: .maven-build
+  variables:
+    MAVEN_PROFILES: "complex-ws,k8s-solr,pub-fallback"
+    PROFILE_SUFFIX: "hx"
+
+maven-build-prod-hh:
+  extends: .maven-build
+  variables:
+    MAVEN_PROFILES: "complex-ws,k8s-solr,pub"
+    PROFILE_SUFFIX: "hh"
+
+.docker-build:
+  stage: build-docker-image
+  before_script:
+    - unset DOCKER_HOST
+    - unset DOCKER_AUTH_CONFIG
+    - docker system prune -af
+  script:
+    - echo "$CI_DOCKER_HUB_PASSWORD" | docker login -u $CI_DOCKER_HUB_USER --password-stdin
+    - echo "$CI_REGISTRY_IMAGE:$IMAGE_TAG"
+    - docker build -t "$CI_REGISTRY_IMAGE:$IMAGE_TAG" --no-cache .
+    - docker image ls
+    - docker logout
+    - echo "$CI_REGISTRY_PASSWORD" | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
+    - docker push "$CI_REGISTRY_IMAGE:$IMAGE_TAG"
+    - docker rmi "$CI_REGISTRY_IMAGE:$IMAGE_TAG"
+    - docker logout $CI_REGISTRY
+
+docker-build-test:
+  extends: .docker-build
+  needs: [ maven-build-test ]
+
+docker-build-prod-hx:
+  extends: .docker-build
+  needs: [ maven-build-prod-hx ]
+
+docker-build-prod-hh:
+  extends: .docker-build
+  needs: [ maven-build-prod-hh ]
+
+.kubernetes-deploy:
+  stage: kubernetes-deploy
+  image: alpine
+  before_script:
+    - apk add --no-cache curl git
+    - curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl
+    - chmod +x ./kubectl
+    - mv ./kubectl /usr/local/bin/kubectl
+    - git clone https://k8s-config-token:$K8S_CONFIG_TOKEN@gitlab.ebi.ac.uk/intact-ci/k8s-config
+    - mkdir ~/.kube
+    - cp k8s-config/config ~/.kube/
+  script:
+    - kubectl config get-contexts
+    - kubectl config use-context $KUBE_CONTEXT
+    - kubectl create secret docker-registry gitlab-registry --docker-server=$CI_REGISTRY --docker-username=$CI_REGISTRY_USER --docker-password=$CI_JOB_TOKEN --docker-email=$GITLAB_USER_EMAIL --dry-run=client -o yaml | kubectl apply -f -
+    - kubectl get secrets gitlab-registry -o yaml
+    - echo "$CI_REGISTRY_IMAGE:$IMAGE_TAG"
+    - sed -i -e "s|<IMAGE_TAG>|$CI_REGISTRY_IMAGE:$IMAGE_TAG|g" k8s-deploy-config/k8s_deploy.yml
+    - sed -i -e "s|<PROXY_HOST>|$PROXY_HOST|g" k8s-deploy-config/k8s_deploy.yml
+    - kubectl apply -f k8s-deploy-config/k8s_deploy.yml
+    - kubectl rollout restart deployment/complex-ws-deployment
+    - kubectl get nodes
+  when: manual
+
+hh-test-deploy:
+  extends: .kubernetes-deploy
+  needs: [ maven-build-test, docker-build-test ]
+  variables:
+    PROXY_HOST: hh-wwwcache.ebi.ac.uk
+    KUBE_CONTEXT: hh-intact-test
+  environment:
+    name: hh/test
+    deployment_tier: testing
+    url: http://hh-rke-wp-webadmin-99-worker-1.caas.ebi.ac.uk:31231/intact/complex-ws
+
+hx-prod-deploy:
+  extends: .kubernetes-deploy
+  needs: [ maven-build-prod-hx, docker-build-prod-hx ]
+  variables:
+    PROXY_HOST: hx-wwwcache.ebi.ac.uk
+    KUBE_CONTEXT: hx-intact-prod
+  environment:
+    name: hx/prod
+    deployment_tier: production
+    url: http://hx-rke-wp-webadmin-78-worker-1.caas.ebi.ac.uk:31231/intact/complex-ws
+
+hh-prod-deploy:
+  extends: .kubernetes-deploy
+  needs: [ maven-build-prod-hh, docker-build-prod-hh ]
+  variables:
+    PROXY_HOST: hh-wwwcache.ebi.ac.uk
+    KUBE_CONTEXT: hh-intact-prod
+  environment:
+    name: hh/prod
+    deployment_tier: production
+    url: http://hh-rke-wp-webadmin-102-worker-1.caas.ebi.ac.uk:31231/intact/complex-ws
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,7 @@
+FROM tomcat:9-jdk11
+
+ADD /target/complex-ws.war "/usr/local/tomcat/webapps/intact#complex-ws.war"
+RUN cp -r webapps.dist/ROOT webapps/
+RUN cp -r webapps.dist/manager webapps/
+
+CMD ["catalina.sh", "run"]
diff --git a/k8s-deploy-config/k8s_deploy.yml b/k8s-deploy-config/k8s_deploy.yml
@@ -0,0 +1,68 @@
+# Specifies what version of K8s you want to use
+apiVersion: v1
+# A service is used to expose your Deployment to the external access
+kind: Service
+metadata:
+  name: complex-ws-service
+spec:
+  ports:
+    - port: 31231
+      protocol: TCP
+      # The port which will be externally exposed. Must be in the range [30000, 32767].
+      nodePort: 31231
+      # The port on your Deployment which it will expose
+      targetPort: 8080
+  selector:
+    # Selects the disease-portal-client Deployment to attach the Service to
+    app: complex-ws
+    # Tell K8s this wants to expose an external port
+  type: NodePort
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: complex-ws-deployment
+spec:
+  selector:
+    matchLabels:
+      app: complex-ws
+  replicas: 1
+  strategy:
+    rollingUpdate:
+      maxSurge: 1
+      maxUnavailable: 0
+    type: RollingUpdate
+  template:
+    metadata:
+      labels:
+        app: complex-ws
+    spec:
+      terminationGracePeriodSeconds: 10
+      restartPolicy: Always
+      containers:
+        - name: complex-ws
+          # Pull the image which contains complex-ws webservice and the built assets from EBI's dockerhub
+          image: <IMAGE_TAG>
+          ports:
+            # We are using complex-ws webservice config which serves on port 8080
+            - containerPort: 8080
+          readinessProbe:
+            tcpSocket:
+              port: 8080
+            initialDelaySeconds: 5
+            periodSeconds: 10
+          livenessProbe:
+            tcpSocket:
+              port: 8080
+            initialDelaySeconds: 15
+            periodSeconds: 20
+          env:
+            - name: http_proxy
+              value: "http://<PROXY_HOST>:3128"
+            - name: https_proxy
+              value: "http://<PROXY_HOST>:3128"
+            - name: JAVA_OPTS
+              value: "-Dhttp.proxyHost=<PROXY_HOST> -Dhttp.proxyPort=3128 -Dhttps.proxyHost=<PROXY_HOST> -Dhttps.proxyPort=3128"
+      imagePullSecrets:
+        # Provided by GitLab, this allows K8s to connect to dockerhub.ebi.ac.uk
+        - name: gitlab-registry
diff --git a/pom.xml b/pom.xml
@@ -281,7 +281,7 @@
     </dependencies>
 
     <build>
-        <finalName>${project.artifactId}-${project.version}</finalName>
+        <finalName>${project.artifactId}</finalName>
 
         <plugins>
             <plugin>

diff --git a/settings.xml b/settings.xml
@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
+          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+          xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 http://maven.apache.org/xsd/settings-1.0.0.xsd">
+
+    <profiles>
+        <profile>
+            <id>complex-ws</id>
+            <properties>
+                <mvn.db.user>${env.CI_POSTGRES_RO_USER}</mvn.db.user>
+                <mvn.db.password>${env.CI_POSTGRES_RO_PASS}</mvn.db.password>
+                <mvn.db.hbm2ddl>none</mvn.db.hbm2ddl>
+                <mvn.db.dialect>org.hibernate.dialect.PostgreSQL82Dialect</mvn.db.dialect>
+                <mvn.db.driver>org.postgresql.Driver</mvn.db.driver>
+                <mvn.solr.maxConnHost>32</mvn.solr.maxConnHost>
+                <mvn.solr.maxConnTotal>128</mvn.solr.maxConnTotal>
+                <mvn.solr.socketTimeOut>20000</mvn.solr.socketTimeOut>
+                <mvn.solr.connectionTimeOut>20000</mvn.solr.connectionTimeOut>
+            </properties>
+        </profile>
+        <profile>
+            <id>k8s-solr</id>
+            <properties>
+                <mvn.solr.url>http://tomcat-solr-service:8080/solr/core_complex_pub/</mvn.solr.url>
+            </properties>
+        </profile>
+        <profile>
+            <id>test</id>
+            <properties>
+                <mvn.db.url>jdbc:postgresql://pgsql-dlvm-085.ebi.ac.uk:5432/intacttst</mvn.db.url>
+                <mvn.intact.graph.ws.url>https://wwwdev.ebi.ac.uk/intact/ws/graph/</mvn.intact.graph.ws.url>
+            </properties>
+        </profile>
+        <profile>
+            <id>pub</id>
+            <properties>
+                <mvn.db.url>jdbc:postgresql://pgsql-dlvmpub2-014.ebi.ac.uk:5432/intactpub</mvn.db.url>
+                <mvn.intact.graph.ws.url>https://www.ebi.ac.uk/intact/ws/graph/</mvn.intact.graph.ws.url>
+            </properties>
+        </profile>
+        <profile>
+            <id>pub-fallback</id>
+            <properties>
+                <mvn.db.url>jdbc:postgresql://pgsql-dlvmpubfall2-011.ebi.ac.uk:5432/intactpub</mvn.db.url>
+                <mvn.intact.graph.ws.url>https://www.ebi.ac.uk/intact/ws/graph/</mvn.intact.graph.ws.url>
+            </properties>
+        </profile>
+        <profile>
+            <id>unit-tests</id>
+            <properties>
+                <mvn.solr.url>http://hh-rke-wp-webadmin-99-worker-1.caas.ebi.ac.uk:31236/solr//core_complex_pub/</mvn.solr.url>
+                <mvn.db.url>jdbc:postgresql://pgsql-dlvm-084.ebi.ac.uk:5432/intactdev</mvn.db.url>
+            </properties>
+        </profile>
+    </profiles>
+</settings>
diff --git a/src/main/java/uk/ac/ebi/intact/service/complex/ws/ComplexCovariationManager.java b/src/main/java/uk/ac/ebi/intact/service/complex/ws/ComplexCovariationManager.java
@@ -23,8 +23,6 @@
 import uk.ac.ebi.intact.service.complex.ws.model.IntactProteinPairScoreDistribution;
 import uk.ac.ebi.intact.service.complex.ws.utils.IntactComplexUtils;
 
-import javax.naming.InitialContext;
-import javax.naming.NamingException;
 import javax.persistence.Query;
 import java.io.IOException;
 import java.net.URI;
@@ -57,9 +55,7 @@ public class ComplexCovariationManager {
     private final String intactProteinScoresEndpointUrl;
     private final String intactProteinScoreDistributionEndpointUrl;
 
-    public ComplexCovariationManager(IntactDao intactDao, @Value("${intact.graph.ws.url}") String intactGraphWsUrlProperty) {
-        String intactGraphWebServiceUrl = getIntactGraphWsUrl(intactGraphWsUrlProperty);
-
+    public ComplexCovariationManager(IntactDao intactDao, @Value("${intact.graph.ws.url}") String intactGraphWebServiceUrl) {
         this.intactDao = intactDao;
         this.client = HttpClient.newBuilder().version(HttpClient.Version.HTTP_1_1).build();
         this.mapper = new ObjectMapper();
@@ -352,12 +348,4 @@ private static String encodeParams(Map<String, String> data) {
         }
         return "?" + sj;
     }
-
-    private static String getIntactGraphWsUrl(String urlFromProperties) {
-        try {
-            return InitialContext.doLookup("java:comp/env/intact.graph.ws.url");
-        } catch (NamingException e) {
-            return urlFromProperties;
-        }
-    }
 }
diff --git a/src/main/resources/complex.properties b/src/main/resources/complex.properties
@@ -5,18 +5,6 @@ db.driver=${mvn.db.driver}
 db.url=${mvn.db.url}
 db.user=${mvn.db.user}
 db.password=${mvn.db.password}
-db.jndi=${mvn.db.intact.jndi}
-
-# solr properties
-solr.complex.url=${mvn.solr.complex.url}
-solr.ontology.url=${mvn.solr.ontology.url}
-
-# intact beans properties
-intact.init.autoPersist=${mvn.intact.init.autoPersist}
-intact.acprefix=${mvn.intact.acprefix}
-intact.db.hbm2ddl=${mvn.intact.db.hbm2ddl}
-intact.db.dialect=${mvn.intact.db.dialect}
-ac.prefix=${mvn.intact.acprefix}
 
 # web services
 intact.graph.ws.url=${mvn.intact.graph.ws.url}
diff --git a/src/main/webapp/WEB-INF/complex-ws-servlet.xml b/src/main/webapp/WEB-INF/complex-ws-servlet.xml
@@ -71,15 +71,12 @@
     </bean>
 
     <!-- Intact core basic datasource -->
-    <bean id="jamiCoreDataSource" class="org.springframework.jndi.JndiObjectFactoryBean">
-        <property name="jndiName" value="java:comp/env/${db.jndi}"/>
+    <bean id="jamiCoreDataSource" class="org.apache.commons.dbcp.BasicDataSource">
+        <property name="driverClassName" value="${db.driver}"/>
+        <property name="url" value="${db.url}"/>
+        <property name="username" value="${db.user}"/>
+        <property name="password" value="${db.password}"/>
     </bean>
-<!--    <bean id="jamiCoreDataSource" class="org.apache.commons.dbcp.BasicDataSource">-->
-<!--        <property name="driverClassName" value="${db.driver}"/>-->
-<!--        <property name="url" value="${db.url}"/>-->
-<!--        <property name="username" value="${db.user}"/>-->
-<!--        <property name="password" value="${db.password}"/>-->
-<!--    </bean>-->
 
     <!-- INTACT more specific beans -->
     <bean id="jamiUserContext" class="uk.ac.ebi.intact.jami.context.UserContext" scope="prototype">

diff --git a/src/main/webapp/WEB-INF/web.xml b/src/main/webapp/WEB-INF/web.xml
@@ -21,9 +21,4 @@
 		<url-pattern>/</url-pattern>
 	</servlet-mapping>
 
-    <resource-env-ref>
-        <resource-env-ref-name>jdbc/IntactDS</resource-env-ref-name>
-        <resource-env-ref-type>javax.sql.DataSource</resource-env-ref-type>
-    </resource-env-ref>
-
 </web-app>
diff --git a/src/test/java/uk/ac/ebi/intact/service/complex/ws/ComplexManagerTest.java b/src/test/java/uk/ac/ebi/intact/service/complex/ws/ComplexManagerTest.java
@@ -297,7 +297,8 @@ private ComplexDetails.ComplexDetailsBuilder expectedComplexDetailsBuilder(
                 .diseases(List.of())
                 .agonists(List.of())
                 .antagonists(List.of())
-                .comments(List.of());
+                .comments(List.of())
+                .releaseDates(List.of());
     }
 
     private IntactComplex buildComplex(