Gandalf plater

helm/gandalf/ncats-images-meta.yaml

@@ -1,3 +1,9 @@
+plater:
+  image: "ghcr.io/translatorsri/plater-clustered"
+  version: "v2.1.4"
+neo4j:
+  image: "ghcr.io/translatorsri/plater-neo4j"
+  version: "neo4j-5.26"
 busybox:
   image: "busybox"
   version: "1.35"

helm/gandalf/templates/configmap.yaml

@@ -8,10 +8,10 @@ data:
   GRAPH_DB: "{{ .Values.graph.backend }}"
   GRAPH_QUERY_TIMEOUT: "{{ .Values.app.GRAPH_QUERY_TIMEOUT }}"
 
-  # turn off automat logic
-  # GANDALF_SERVICE_ADDRESS: "{{ include "gandalf.fullname" . }}-service"
-  # GANDALF_AUTOMAT_HOST: {{ .Values.app.automatAddress }}
-  # GANDALF_PLATER_TITLE: {{ .Release.Name }}
+  # Enable automat registration
+  GANDALF_SERVICE_ADDRESS: "{{ include "gandalf.fullname" . }}-service"
+  GANDALF_AUTOMAT_HOST: {{ .Values.app.automatAddress }}
+  GANDALF_PLATER_TITLE: {{ .Release.Name }}
   GANDALF_INFORES: "{{ .Values.datasetDesc.provenanceTag }}"
   BL_VERSION: "{{ .Values.app.bl_version }}"
   GANDALF_SERVER_MATURITY: "{{ .Values.x_trapi.maturity.value }}"

helm/gandalf/templates/gandalf-loader.yaml

@@ -97,6 +97,21 @@ spec:
       nodeSelector:
         {{- toYaml . | nindent 8 }}
       {{- end }}
+      {{- with .Values.app.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- else }}
+      {{- if and (eq .Values.graph.backend "gandalf") (not .Values.graph.external) }}
+      # Force loader to run on same node as the PVC (RWO volume constraint)
+      affinity:
+        podAffinity:
+          requiredDuringSchedulingIgnoredDuringExecution:
+            - labelSelector:
+                matchLabels:
+                  {{- include "gandalf.selectorLabels" . | nindent 18 }}
+              topologyKey: kubernetes.io/hostname
+      {{- end }}
+      {{- end }}
       {{- with .Values.app.tolerations }}
       tolerations:
         {{- toYaml . | nindent 8 }}

helm/gandalf/templates/ingress.yaml

@@ -1,3 +1,4 @@
+{{- if .Values.ingress.enabled -}}
 {{- if and .Values.ingress.class (not (semverCompare ">=1.18-0" .Capabilities.KubeVersion.GitVersion)) }}
   {{- if not (hasKey .Values.ingress.gandalf.annotations "kubernetes.io/ingress.class") }}
   {{- $_ := set .Values.ingress.gandalf.annotations "kubernetes.io/ingress.class" .Values.ingress.class }}
@@ -48,3 +49,4 @@ spec:
             serviceName: {{ include "gandalf.fullname" . }}-service
             servicePort: {{ .Values.app.gandalf.service.port }}
             {{- end }}
+{{- end -}}

helm/gandalf/values.yaml

@@ -24,7 +24,7 @@ image:
     tag: 0.3.3
     pullPolicy: Always
 
-nameOverride: ""
+nameOverride: "plater"
 fullnameOverride: ""
 
 app:
@@ -81,7 +81,7 @@ app:
           ephemeral-storage: "6Gi"
     persistentVolume:
       accessModes: 
-        - ReadWriteMany
+        - ReadWriteOnce
       size: "5Gi"
 
   openapi_config:

jenkins/gandalf/Jenkinsfile

@@ -0,0 +1,171 @@
+pipeline {
+    options {
+        timestamps()
+        skipDefaultCheckout()
+        disableConcurrentBuilds()
+    }
+    agent {
+        node { label 'translator && aws && build' }
+    }
+    parameters {
+        string(name: 'BUILD_VERSION', defaultValue: '', description: 'The build version to deploy (optional)')
+        choice(name: 'PLATERS', choices: 'all\nhgnc\ncam-kp\nicees-kg\nmonarch-kg\nrobokopkg\n', description: 'Platers to deploy')
+        choice(name: 'ACTION', choices: 'install\ndelete', description: 'Install or delete, default install')
+        string(name: 'AWS_REGION', defaultValue: 'us-east-1', description: 'AWS Region to deploy')
+        string(name: 'KUBERNETES_CLUSTER_NAME', defaultValue: 'translator-eks-ci-blue-cluster', description: 'AWS EKS that will host this application')
+    }
+    triggers {
+        pollSCM('H/2 * * * *')
+    }
+    environment {
+        DEPLOY_ENV = "dev"
+    }
+    stages {
+        stage('Clean') {
+            steps {
+                cleanWs()
+                checkout scm
+            }
+        }
+        stage('Build Version') {
+            when {
+                allOf {
+                    expression {
+                        return !params.BUILD_VERSION
+                    }
+                    anyOf {
+                        changeset "helm/gandalf/**"
+                        triggeredBy 'UserIdCause'
+                    }
+                }
+            }
+            steps{
+               script {
+                    def imageMeta = readYaml file: 'helm/gandalf/ncats-images-meta.yaml'
+                    env.ORIGINAL_REPO = imageMeta.plater.image
+                    env.BUILD_VERSION = imageMeta.plater.version
+                    env.ORIGINAL_REPO_NEO4J = imageMeta.neo4j.image
+                    env.BUILD_VERSION_NEO4J = imageMeta.neo4j.version
+                    env.ORIGINAL_REPO_BUSYBOX = imageMeta.busybox.image
+                    env.BUILD_VERSION_BUSYBOX = imageMeta.busybox.version
+                    currentBuild.displayName = imageMeta.plater.version + "#" + imageMeta.neo4j.version
+              }
+           }
+        }
+        stage('build image') {
+            when {
+                allOf {
+                    expression {
+                        return !params.BUILD_VERSION
+                    }
+                    anyOf {
+                        changeset "helm/gandalf/**"
+                        triggeredBy 'UserIdCause'
+                    }
+                }
+            }
+            steps {
+                withEnv([
+                    "IMAGE_NAME=translator-sri-plater-clustered",
+                    "BUILD_VERSION=" + (params.BUILD_VERSION ? params.BUILD_VERSION.tokenize("#")[0] : env.BUILD_VERSION)
+                ]) {
+                    dir("helm/gandalf") {
+                        script {
+
+                            sh '''
+                            docker pull $ORIGINAL_REPO:$BUILD_VERSION
+                            docker tag $ORIGINAL_REPO:$BUILD_VERSION 853771734544.dkr.ecr.us-east-1.amazonaws.com/$IMAGE_NAME:$BUILD_VERSION
+                            '''
+                            def image = docker.image("853771734544.dkr.ecr.us-east-1.amazonaws.com/$IMAGE_NAME:$BUILD_VERSION")
+                            sh '''
+                            aws ecr get-login-password --region us-east-1 | docker login --username AWS --password-stdin  853771734544.dkr.ecr.us-east-1.amazonaws.com
+                            '''
+                                image.push()
+                        }
+                    }
+                }
+                withEnv([
+                    "IMAGE_NAME=translator-sri-neo4j-42-apoc-gds",
+                    "BUILD_VERSION=" + (params.BUILD_VERSION ? params.BUILD_VERSION.tokenize("#")[1] : env.BUILD_VERSION_NEO4J)
+                ]) {
+                    dir("helm/gandalf") {
+                        script {
+
+                            sh '''
+                            docker pull $ORIGINAL_REPO_NEO4J:$BUILD_VERSION_NEO4J
+                            docker tag $ORIGINAL_REPO_NEO4J:$BUILD_VERSION_NEO4J 853771734544.dkr.ecr.us-east-1.amazonaws.com/$IMAGE_NAME:$BUILD_VERSION
+                            '''
+                            def image = docker.image("853771734544.dkr.ecr.us-east-1.amazonaws.com/$IMAGE_NAME:$BUILD_VERSION")
+                            sh '''
+                            aws ecr get-login-password --region us-east-1 | docker login --username AWS --password-stdin  853771734544.dkr.ecr.us-east-1.amazonaws.com
+                            '''
+                                image.push()
+                        }
+                    }
+                }
+                withEnv([
+                    "IMAGE_NAME=translator-busybox"
+                ]) {
+                    dir("helm/gandalf") {
+                        script {
+
+                            sh '''
+                            docker pull $ORIGINAL_REPO_BUSYBOX:stable
+                            docker pull $ORIGINAL_REPO_BUSYBOX:latest
+                            docker tag $ORIGINAL_REPO_BUSYBOX:stable 853771734544.dkr.ecr.us-east-1.amazonaws.com/$IMAGE_NAME:stable
+                            docker tag $ORIGINAL_REPO_BUSYBOX:latest 853771734544.dkr.ecr.us-east-1.amazonaws.com/$IMAGE_NAME:latest
+                            '''
+                            def image = docker.image("853771734544.dkr.ecr.us-east-1.amazonaws.com/$IMAGE_NAME:stable")
+                            def imageLatest = docker.image("853771734544.dkr.ecr.us-east-1.amazonaws.com/$IMAGE_NAME:latest")
+
+                            sh '''
+                            aws ecr get-login-password --region us-east-1 | docker login --username AWS --password-stdin  853771734544.dkr.ecr.us-east-1.amazonaws.com
+                            '''
+                                image.push()
+                                imageLatest.push()
+                        }
+                    }
+                }
+            }
+        }
+        stage('Deploy') {
+            agent {
+                label 'translator && ci && deploy'
+            }
+            when {
+                anyOf {
+                    changeset "helm/gandalf/**"
+                    triggeredBy 'UserIdCause'
+                }
+            }
+            steps {
+                checkout scm
+                dir('helm/gandalf') {
+                    configFileProvider([
+                        configFile(fileId: 'gandalf-plater.sh', targetLocation: 'prepare.sh'),
+                        configFile(fileId: 'values-plater.yaml', targetLocation: 'values-plater.yaml'),
+                        configFile(fileId: 'gandalf-deploy.sh', targetLocation: 'deploy.sh')
+                    ]){
+                        withEnv([
+                            "BUILD_VERSION_PLATER=" + (params.BUILD_VERSION ? params.BUILD_VERSION.tokenize("#")[0] : env.BUILD_VERSION),
+                            "BUILD_VERSION_NEO4J=" + (params.BUILD_VERSION ? params.BUILD_VERSION.tokenize("#")[1] : env.BUILD_VERSION_NEO4J),
+                            "PLATERS=" + params.PLATERS,
+                            "ACTION=" + params.ACTION
+                        ]) {
+                            sh '''
+                                aws --region ${AWS_REGION} eks update-kubeconfig --name ${KUBERNETES_CLUSTER_NAME}
+                                /bin/bash prepare.sh
+                            '''
+                        }
+                    }
+                }
+            }
+            post {
+                always {
+                    echo " Clean up the workspace in deploy node!"
+                    cleanWs()
+                }
+            }
+        }
+    }
+}