Merge branch 'beta' into 'master'

New Cluster

See merge request !8

.gitlab-ci.yml

@@ -97,3 +97,4 @@ Dev-API Kube deploy:
   only:
     refs:
       - dev
+      #

cbioondemandK8S/src/main/java/cz/muni/ics/edirex/cbioondemandK8S/service/KubernetesImpl.java

@@ -37,14 +37,14 @@ public class KubernetesImpl implements CBioOnDemandService {
     private V1beta1CronJob cronJob;
     private IdentifierCRD identifier;
 
-    @Value("${namespace:cbio-on-demand}")
-    private final String NAMESPACE = "cbio-on-demand";
+    private final String NAMESPACE;
     private final String APP_LABELS = "app=cbio, type=ondemand";
     private final String DB_LABELS = "app=cbioDB, type=ondemand";
 
-    public KubernetesImpl(KubernetesCalls api, RoutingAAI routing) throws IOException {
+    public KubernetesImpl(KubernetesCalls api, RoutingAAI routing, @Value("${namespace:cbio-on-demand}")String namespace) throws IOException {
         this.api = api;
         this.routing = routing;
+        NAMESPACE = namespace;
         cronJob = (V1beta1CronJob) Utils.getConfigurationFromYaml("deletecronjob.yml");
         cbioService = (V1Service) Utils.getConfigurationFromYaml("cbio-service.yml");
         cbioReplicaSet = (V1ReplicaSet) Utils.getConfigurationFromYaml("cbio-replicaset.yml");

cbioondemandK8S/src/main/resources/cbio-replicaset.yml

@@ -28,6 +28,20 @@ spec:
         # generated by API unique for user
         #instance: "1"
     spec:
+      tolerations:
+        - effect: NoSchedule
+          key: edirex
+          operator: Equal
+          value: cbio
+      affinity:
+        nodeAffinity:
+          requiredDuringSchedulingIgnoredDuringExecution:
+            nodeSelectorTerms:
+              - matchExpressions: 
+                - key: edirex
+                  operator: In
+                  values: 
+                  - cbio
       initContainers:
         - name: wait-for-db
           image: lpivo/wait_for_db:tr2
@@ -39,7 +53,7 @@ spec:
         - name: dataloding
       containers:
         - name: cbio
-          image: registry.gitlab.ics.muni.cz:443/europdx/k8s/cbio-on-demand/data-loading:app32a8fb32ad9831d51a829bb4583375b21ba511e1
+          image: registry.gitlab.ics.muni.cz:443/europdx/k8s/cbio-on-demand/data-loading:master-app-97fb8c1069486ec071efbca7809303c5c5203b46 
           ports:
             - name: http
               containerPort: 8080
@@ -48,7 +62,7 @@ spec:
               # generated by API from service name
               value: cbio-on-demand-dbpjvrw
             - name: IMPORT
-              value: /etc/data-loading/cbio-client.py
+              value: /etc/data-loading/cbio_client.py
             - name: ID
               # generated by API from user request
               value: "4"
@@ -57,7 +71,12 @@ spec:
               value: cbioportal
             - name: URL
               value: 'test'
+            - name: DATAHUB
+              valueFrom:
+                configMapKeyRef:
+                  name: app
+                  key: datahub
           lifecycle:
             postStart:
               exec:
-                command: ["python3", "/etc/data-loading/cbio-client.py"]
+                command: ["python3", "/etc/data-loading/cbio_client.py"]

cbioondemandK8S/src/main/resources/cbiodb-replicaset.yml

@@ -28,6 +28,20 @@ spec:
         # generated by API unique for user
         #instance: "1"
     spec:
+      tolerations:
+          - effect: NoSchedule
+            key: edirex
+            operator: Equal
+            value: cbio
+      affinity:
+        nodeAffinity:
+          requiredDuringSchedulingIgnoredDuringExecution:
+            nodeSelectorTerms:
+              - matchExpressions: 
+                - key: edirex
+                  operator: In
+                  values: 
+                  - cbio
       containers:
         - name: cbio
           image: lpivo/cbiodb:v1

k8s/deployment.yml

@@ -21,6 +21,25 @@ spec:
         app: cbio-api
         type: ondemand
     spec:
+      tolerations:
+        - effect: NoSchedule
+          key: node-role.kubernetes.io/controlplane
+          operator: Equal
+          value: "true"
+        - effect: NoExecute
+          key: node-role.kubernetes.io/etcd
+          operator: Equal
+          value: "true"
+      affinity:
+        nodeAffinity:
+          requiredDuringSchedulingIgnoredDuringExecution:
+            nodeSelectorTerms:
+              - matchExpressions: 
+                - key: node-role.kubernetes.io/controlplane
+                  operator: In
+                  values: 
+                  - "true"
+      serviceAccountName: cbio-api
       imagePullSecrets:
         - name: temporary
       containers: