config-editor-20230505160307.tar.gz

./000755 000766 000024 00000000000 14427434024 011633 5ustar00dweberstaff000000 000000 ./Docker/000755 000766 000024 00000000000 14427161347 013047 5ustar00dweberstaff000000 000000 ./Kubernetes/000755 000766 000024 00000000000 14341214157 013740 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/000755 000766 000024 00000000000 14317125417 016671 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/cdc/000755 000766 000024 00000000000 14321273233 017415 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/crtg/000755 000766 000024 00000000000 14321273261 017624 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/crtg/chart/000755 000766 000024 00000000000 14321273172 020726 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/crtg/chart/crtg/000755 000766 000024 00000000000 14417557453 021702 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/crtg/chart/crtg/Chart.yaml000644 000766 000024 00000000172 14317125246 023615 0ustar00dweberstaff000000 000000 apiVersion: v2
appVersion: "2.0"
description: A Helm chart for Kubernetes
name: merative-acd-ce-crtg-chart
version: 2.0.0
./Kubernetes/merative-acd-ce/crtg/chart/crtg/nginx-server.conf000644 000766 000024 00000001372 14341215732 025166 0ustar00dweberstaff000000 000000 server {
  listen 8080;
  listen [::]:8080;

  listen 9444 ssl;
  listen [::]:9444 ssl;
  ssl_protocols TLSv1.2;
  ssl_certificate /tmp/keystore/tls.crt;
  ssl_certificate_key /tmp/keystore/tls.key;

  access_log /var/log/nginx/access.log;
  error_log /var/log/nginx/error.log warn;

  server_name localhost;
  proxy_connect_timeout 120;
  client_max_body_size 10M;

  location /nginx_status {
      stub_status;
      allow 127.0.0.1; #only allow requests from localhost
      allow ::1; #only allow requests from localhost
      deny all;	#deny all other hosts
  }
  location /services/cartridge/ {
      proxy_ssl_server_name on;
      proxy_set_header  X-Auth-Request-Email $http_x_forwarded_email;
      proxy_pass https://127.0.0.1:9443$request_uri;
  }
}
./Kubernetes/merative-acd-ce/crtg/chart/crtg/templates/000755 000766 000024 00000000000 14422030320 023647 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/crtg/chart/crtg/values.yaml000644 000766 000024 00000001536 14425266642 024066 0ustar00dweberstaff000000 000000 annotations:
  TOOLCHAIN_ID: ""
  GIT_URL: ""
  GIT_BRANCH: ""
  GIT_COMMIT: ""
  USER_NAME: ""
  APPLICATION_VERSION: ""
configurationStorage:
  backend: file
  sharedPrefix: tenant_data/ibm_supertenant
  tenantPrefix: tenant_data
  s3:
    bucket: ""
    endpointUrl: ""
    location: ""
  file:
    persistent: true
    volume:
      existingClaimName: ""
      supplementalGroup: ""
container:
  image: acdcontaineredition.azurecr.io/acd-ce/cartridge 
  digest: 9cc9bec2070af7aacc749952f18186d3f132c8e8f5b0c688b7407ad5163ad7f9
  tag: "20230504.1750"
networkPolicy:
  ingress:
    fromSelectors: ""
revProxy:
  image: nginxinc/nginx-unprivileged:stable
revProxyTargets:
replicas: 1
resources:
  limits:
    cpu: ""
    ephemeralStorage: 1100Mi
    memory: 2G
  requests:
    cpu: 100m
    ephemeralStorage: 900Mi
    memory: 2G
tenantHeader:
tolerations: []

./Kubernetes/merative-acd-ce/crtg/chart/crtg/templates/networkpolicy-acd-microservice.yaml000644 000766 000024 00000001555 14341444250 032702 0ustar00dweberstaff000000 000000 kind: NetworkPolicy
apiVersion: networking.k8s.io/v1
metadata:
  name: acd-ce-acd-microservice
  namespace: {{ .Release.Namespace }}
  labels:
    app.kubernetes.io/name: acd-ce-acd-microservice
    app.kubernetes.io/instance: acd-ce-acd-microservice-{{ .Release.Name }}
    app.kubernetes.io/managed-by: helm
    app.kubernetes.io/version: "2.0.0"
    helm.sh/chart: merative-acd-chart
spec:
  podSelector:
    matchLabels:
      acd/serviceType: microservice
  ingress:
    - ports:
        - protocol: TCP
          port: 9443
      from:
        # This rule will only allow the macro ACD service to connect to
        # the microservices in this namespace.
        - podSelector:
            matchLabels:
              acd/serviceType: macroservice
        - podSelector:
            matchLabels:
              acd-ce/serviceType: macroservice
  policyTypes:
    - Ingress
./Kubernetes/merative-acd-ce/crtg/chart/crtg/templates/deployment.yaml000644 000766 000024 00000036564 14422310442 026737 0ustar00dweberstaff000000 000000 kind: Deployment
apiVersion: apps/v1
metadata:
  name: merative-acd-crtg
  namespace: {{ .Release.Namespace }}
  labels:
    app.kubernetes.io/name: merative-acd-crtg
    app.kubernetes.io/instance: merative-acd-crtg-{{ .Release.Name }}
    app.kubernetes.io/managed-by: Helm
    app.kubernetes.io/part-of: merative-acd-ce
    app.kubernetes.io/version: "2.0.0"
    helm.sh/chart: merative-acd-chart
  annotations:
    TOOLCHAIN_ID: "{{ .Values.annotations.TOOLCHAIN_ID }}"
    GIT_URL: "{{ .Values.annotations.GIT_URL }}"
    GIT_BRANCH: "{{ .Values.annotations.GIT_BRANCH }}"
    GIT_COMMIT: "{{ .Values.annotations.GIT_COMMIT }}"
    USER_NAME: "{{ .Values.annotations.USER_NAME }}"
    APPLICATION_VERSION: "{{ .Values.annotations.APPLICATION_VERSION }}"
spec:
  replicas: {{ .Values.replicas }}
  selector:
    matchLabels:
      app.kubernetes.io/name: merative-acd-crtg
  strategy:
    type: RollingUpdate
    rollingUpdate:
      maxSurge: "25%"
      maxUnavailable: "25%"
  template:
    metadata:
      annotations:
        productID: ""
        productName: ""
        productVersion: 2.0.0
        productMetric: VIRTUAL_PROCESSOR_CORE
        productChargedContainers: ""
      creationTimestamp:
      labels:
        app.kubernetes.io/context: cartridge
        app.kubernetes.io/instance: merative-acd-crtg-{{ .Release.Name }}
        app.kubernetes.io/managed-by: Helm
        app.kubernetes.io/name: merative-acd-crtg
        app.kubernetes.io/part-of: merative-acd-ce
        app.kubernetes.io/version: "2.0.0"
        app.kubernetes.io/versionedApp: merative-acd-crtg-{{ .Values.container.tag }}
        helm.sh/chart: merative-acd-chart
        acd-ce/serviceType: macroservice
    spec:
      hostNetwork: false
      hostPID: false
      hostIPC: false
      imagePullSecrets:
        - name: artifactory.commops.merative.com
      containers:
        - name: merative-acd-crtg
          image: {{ .Values.container.image }}@sha256:{{ .Values.container.digest }}
          env:
            - name: "clinical_data_annotator_car_acd_sandbox_url"
              value: "https://merative-acd-acd.{{ .Release.Namespace }}:443/services/clinical_data_annotator"
            - name: "clinical_data_annotator_car_acd_target_url"
              value: "https://merative-acd-acd.{{ .Release.Namespace }}:443/services/clinical_data_annotator"
            - name: "clinical_data_annotator_car_aci_url"
              value: "https://merative-acd-aci.{{ .Release.Namespace }}:443/services/advanced_care_insights"
            - name: "clinical_data_annotator_car_av_url"
              value: "https://merative-acd-av.{{ .Release.Namespace }}:443/services/attribute_detection"
            - name: "clinical_data_annotator_car_url"
              value: "https:///merative-acd-crtg.{{ .Release.Namespace }}:443/services/cartridge"
            - name: "clinical_data_annotator_car_cd_url"
              value: "https://merative-acd-cd.{{ .Release.Namespace }}:443/services/concept_detection"
            - name: "clinical_data_annotator_car_cdc_url"
              value: "https://merative-acd-cdc.{{ .Release.Namespace }}:443/services/concept_dictionary"
            - name: "clinical_data_annotator_car_cds_url"
              value: "https://merative-acd-cds.{{ .Release.Namespace }}:443/services/concept_disambiguation"
            - name: "clinical_data_annotator_car_hyp_url"
              value: "https://merative-acd-hyp.{{ .Release.Namespace }}:443/services/hypothetical_detection"
            - name: "clinical_data_annotator_car_neg_url"
              value: "https://merative-acd-neg.{{ .Release.Namespace }}:443/services/negation_detection"
            - name: "clinical_data_annotator_car_ont_url"
              value: "https://merative-acd-ont.{{ .Release.Namespace }}:443/services/ontology"
            - name: "clinical_data_annotator_car_spl_url"
              value: "https://merative-acd-spl.{{ .Release.Namespace }}:443/services/spell_checker"
            - name: "clinical_data_annotator_car_acd_sandbox_internal_url"
              value: "https://merative-acd-acd.{{ .Release.Namespace }}:443/services/clinical_data_annotator"
            - name: "clinical_data_annotator_car_acd_target_internal_url"
              value: "https://merative-acd-acd.{{ .Release.Namespace }}:443/services/clinical_data_annotator"
            - name: "clinical_data_annotator_car_aci_internal_url"
              value: "https://merative-acd-aci.{{ .Release.Namespace }}:443/services/advanced_care_insights"
            - name: "clinical_data_annotator_car_av_internal_url"
              value: "https://merative-acd-av.{{ .Release.Namespace }}:443/services/attribute_detection"
            - name: "clinical_data_annotator_car_cd_internal_url"
              value: "https://merative-acd-cd.{{ .Release.Namespace }}:443/services/concept_detection"
            - name: "clinical_data_annotator_car_cdc_internal_url"
              value: "https://merative-acd-cdc.{{ .Release.Namespace }}:443/services/concept_dictionary"
            - name: "clinical_data_annotator_car_cds_internal_url"
              value: "https://merative-acd-cds.{{ .Release.Namespace }}:443/services/concept_disambiguation"
            - name: "clinical_data_annotator_car_hyp_internal_url"
              value: "https://merative-acd-hyp.{{ .Release.Namespace }}:443/services/hypothetical_detection"
            - name: "clinical_data_annotator_car_neg_internal_url"
              value: "https://merative-acd-neg.{{ .Release.Namespace }}:443/services/negation_detection"
            - name: "clinical_data_annotator_car_ont_internal_url"
              value: "https://merative-acd-ont.{{ .Release.Namespace }}:443/services/ontology"
            - name: "clinical_data_annotator_car_spl_internal_url"
              value: "https://merative-acd-spl.{{ .Release.Namespace }}:443/services/spell_checker"
            - name: "clinical_data_annotator_car_auth_header_email"
              value: 
            - name: "clinical_data_annotator_artifactstore_shared_backend"
              value: "{{ .Values.configurationStorage.backend }}"
            - name: "clinical_data_annotator_artifactstore_tenant_backend"
              value: "{{ .Values.configurationStorage.backend }}"
            - name: "clinical_data_annotator_artifactstore_tenant_prefix"
              value: "{{ .Values.configurationStorage.tenantPrefix }}"
            - name: "clinical_data_annotator_artifactstore_shared_prefix"
              value: "{{ .Values.configurationStorage.sharedPrefix }}"
            - name: "clinical_data_annotator_artifactstore_cos_buckets"
              value: "{{ .Values.configurationStorage.s3.bucket }}"
            - name: "clinical_data_annotator_artifactstore_cos_tenants"
              value: "wh-acd"
            - name: "clinical_data_annotator_artifactstore_cos_accessKeyIdFiles"
              value: "ibm_wh_acd_as/username"
            - name: "clinical_data_annotator_artifactstore_cos_accessKeySecretFiles"
              value: "ibm_wh_acd_as/password"
            - name: "clinical_data_annotator_artifactstore_cos_endpointUrl"
              value: "{{ .Values.configurationStorage.s3.endpointUrl }}"
            - name: "clinical_data_annotator_artifactstore_cos_location"
              value: "{{ .Values.configurationStorage.s3.location }}"
            - name: "clinical_data_annotator_common_client_auth_enabled"
              value: "false"
            - name: "clinical_data_annotator_common_concurrent_blocking_threshold"
              value: "10"
            - name: "clinical_data_annotator_common_concurrent_reject_threshold"
              value: "50"
            - name: "clinical_data_annotator_common_concurrent_uri_pattern_list"
              value: "/v1/cartridge.*"
            - name: "clinical_data_annotator_common_context_root"
              value: "services/cartridge"
            - name: "clinical_data_annotator_common_enabled_dark_features"
              value: "{{ .Values.enabledDarkFeatures }}"
            - name: "clinical_data_annotator_common_http_port"
              value: "-1"
            - name: "clinical_data_annotator_common_https_port"
              value: "9443"
            - name: "clinical_data_annotator_common_log_event_format"
              value: "json"
            - name: "clinical_data_annotator_common_max_heap"
              value: "1G"
            - name: "clinical_data_annotator_common_min_heap"
              value: "1G"
            - name: "clinical_data_annotator_common_service_name"
              value: "cartridge"
            - name: "clinical_data_annotator_car_internal_deployment"
              value: "true"
            - name: "clinical_data_annotator_common_shared_config_dir"
              value: "/opt/ibm/watsonhealth/services/config"
            - name: "clinical_data_annotator_car_api_request_timeout_read"
              value: "60000"
            - name: "clinical_data_annotator_car_api_request_timeout_connection"
              value: "5000"
          {{- with .Values.revProxyTargets }}
{{ toYaml . | indent 12 }}
          {{- end }}
            {{- if .Values.tenantHeader }}
            - name: "clinical_data_annotator_services_authentication_type"
              value: "custom_header"
            - name: "clinical_data_annotator_services_authentication_header"
              value: "{{ .Values.tenantHeader }}"
            {{- end }}
          terminationMessagePath: /dev/termination-log
          terminationMessagePolicy: File
          imagePullPolicy: IfNotPresent
          ports:
            - name: crtg-https
              containerPort: 9443
              protocol: TCP
          volumeMounts:
            - name: as-volume
              mountPath: /opt/ibm/watsonhealth/services/config/secrets/ibm_wh_acd_as
              readOnly: true
            - name: certs-keystore-volume
              mountPath: /tmp/keystore
              readOnly: true
            - name: certs-truststore-volume
              mountPath: /opt/ibm/watsonhealth/services/config/certs/truststore
              readOnly: true
            - name: configmap-env-volume
              mountPath: /opt/ibm/watsonhealth/services/config/configmaps
              readOnly: true
          {{- if and (eq .Values.configurationStorage.backend "file") .Values.configurationStorage.file.persistent }}
            - name: {{ .Release.Name }}-file-store-pvc
              mountPath: /opt/ibm/watsonhealth/services/config/artifactstore/tenant_data
              readOnly: false
          {{- end }}
          startupProbe:
            exec:
              command:
                - /staging/whcs-devops-ucd/docker/k8s_startup.sh
            initialDelaySeconds: 30
            timeoutSeconds: 1800
            periodSeconds: 30
            successThreshold: 1
            failureThreshold: 10
          livenessProbe:
            exec:
              command:
                - /staging/whcs-devops-ucd/docker/docker_liveness.sh
            initialDelaySeconds: 5
            periodSeconds: 30
            timeoutSeconds: 10
            failureThreshold: 5
          readinessProbe:
            exec:
              command:
                - /staging/whcs-devops-ucd/docker/docker_readiness.sh
            initialDelaySeconds: 5
            periodSeconds: 60
            timeoutSeconds: 10
            failureThreshold: 1
          resources:
            requests:
              cpu: {{ index .Values.resources.requests.cpu}}
              ephemeral-storage: {{ index .Values.resources.requests "ephemeralStorage" }}
              memory: {{ .Values.resources.requests.memory }}
            limits:
              ephemeral-storage: {{ index .Values.resources.limits "ephemeralStorage" }}
              memory: {{ .Values.resources.limits.memory }}
          securityContext:
            privileged: false
            readOnlyRootFilesystem: false
            allowPrivilegeEscalation: false
            runAsNonRoot: true
          {{- if not (.Capabilities.APIVersions.Has "security.openshift.io/v1") }}
            runAsUser: 1001
          {{- end }}
            capabilities:
              drop: ["ALL"]
        - name: rev-proxy
          image: {{ .Values.revProxy.image }}
          imagePullPolicy: IfNotPresent
          ports:
            - name: crtg-https-pxy
              containerPort: 9444
              protocol: TCP
          resources:
            limits:
              cpu: 300m
              memory: 512Mi
            requests:
              cpu: 200m
              memory: 256Mi
          volumeMounts:
          - name: certs-keystore-volume
            mountPath: /tmp/keystore
            readOnly: true
          - mountPath: /etc/nginx/conf.d
            name: nginx-server
      securityContext:
        runAsNonRoot: true
      {{- if not (.Capabilities.APIVersions.Has "security.openshift.io/v1") }}
        runAsUser: 1001
      {{- end }}
      {{- if eq .Values.configurationStorage.backend "file" }}
        {{- if .Values.configurationStorage.file.volume.supplementalGroup }}
        supplementalGroups: [{{ .Values.configurationStorage.file.volume.supplementalGroup }}]
        {{- end }}
      {{- end }}
      volumes:
      - name: as-volume
        secret:
          secretName: merative-acd-as
          optional: true
      - name: certs-keystore-volume
        secret:
          secretName: merative-acd-crtg-certs-keystore
        {{- if not (.Capabilities.APIVersions.Has "security.openshift.io/v1") }}
          optional: true
        {{- end }}
      - name: certs-truststore-volume
        configMap:
          name: merative-acd-ce-certs-truststore-pem
          optional: true
      - name: configmap-env-volume
        configMap:
          name: merative-acd-custom-env
          optional: true
      - name: {{ .Release.Name }}-file-store-pvc
      {{- if and (eq .Values.configurationStorage.backend "file") .Values.configurationStorage.file.persistent }}
        persistentVolumeClaim:
        {{- if .Values.configurationStorage.file.volume.existingClaimName }}
          claimName: {{ .Values.configurationStorage.file.volume.existingClaimName }}
        {{- else }}
          claimName: {{ .Release.Name }}-file-store-pvc
        {{- end }}
      {{- else }}
        emptyDir: {}
      {{- end }}
      - name: nginx-server
        configMap:
          name: nginx-server
      affinity:
        nodeAffinity:
          requiredDuringSchedulingIgnoredDuringExecution:
            nodeSelectorTerms:
              - matchExpressions:
                - key: kubernetes.io/arch
                  operator: In
                  values:
                    - amd64
        podAntiAffinity:
          preferredDuringSchedulingIgnoredDuringExecution:
          - podAffinityTerm:
              labelSelector:
                matchExpressions:
                - key: app.kubernetes.io/versionedApp
                  operator: In
                  values:
                  - merative-acd-crtg-{{ .Values.container.tag }}
              topologyKey: failure-domain.alpha.kubernetes.io/zone
            weight: 100
          requiredDuringSchedulingIgnoredDuringExecution:
          - labelSelector:
              matchExpressions:
              - key: app.kubernetes.io/versionedApp
                operator: In
                values:
                - merative-acd-crtg-{{ .Values.container.tag }}
            topologyKey: kubernetes.io/hostname
    {{- with .Values.tolerations }}
      tolerations:
{{ toYaml . | indent 8 }}
    {{- end }}
      restartPolicy: Always
      terminationGracePeriodSeconds: 30
      dnsPolicy: ClusterFirst
      dnsConfig:
        options:
          - name: single-request
      schedulerName: default-scheduler
./Kubernetes/merative-acd-ce/crtg/chart/crtg/templates/networkpolicy-acd-macroservice.yaml000644 000766 000024 00000001224 14341444303 032662 0ustar00dweberstaff000000 000000 kind: NetworkPolicy
apiVersion: networking.k8s.io/v1
metadata:
  name: acd-ce-acd-macroservice
  namespace: {{ .Release.Namespace }}
  labels:
    app.kubernetes.io/name: acd-ce-acd-macroservice
    app.kubernetes.io/instance: acd-ce-acd-macroservice-{{ .Release.Name }}
    app.kubernetes.io/managed-by: helm
    app.kubernetes.io/version: "2.0.0"
    helm.sh/chart: merative-acd-chart
spec:
  ingress:
    - ports:
        - port: 9443
          protocol: TCP
      from:
      - podSelector:
          matchLabels:
            acd-ce/serviceType: macroservice
  podSelector:
    matchLabels:
      acd/serviceType: macroservice
  policyTypes:
    - Ingress
./Kubernetes/merative-acd-ce/crtg/chart/crtg/templates/networkpolicy-acd-ingress-deny-all.yaml000644 000766 000024 00000000704 14317125246 033364 0ustar00dweberstaff000000 000000 kind: NetworkPolicy
apiVersion: networking.k8s.io/v1
metadata:
  name: acd-ce-acd-ingress-deny-all
  namespace: {{ .Release.Namespace }}
  labels:
    app.kubernetes.io/name: acd-ce-acd-ingress-deny-all
    app.kubernetes.io/instance: acd-ce-acd-ingress-deny-all-{{ .Release.Name }}
    app.kubernetes.io/managed-by: helm
    app.kubernetes.io/version: "2.0.0"
    helm.sh/chart: merative-acd-chart
spec:
  podSelector: {}
  policyTypes:
    - Ingress
./Kubernetes/merative-acd-ce/crtg/chart/crtg/templates/networkpolicy-macroservice.yaml000644 000766 000024 00000001444 14341444230 032140 0ustar00dweberstaff000000 000000 kind: NetworkPolicy
apiVersion: networking.k8s.io/v1
metadata:
  name: merative-acd-ce-macroservice
  namespace: {{ .Release.Namespace }}
  labels:
    app.kubernetes.io/name: merative-acd-ce-macroservice
    app.kubernetes.io/instance: merative-acd-ce-macroservice-{{ .Release.Name }}
    app.kubernetes.io/managed-by: helm
    app.kubernetes.io/version: "2.0.0"
    helm.sh/chart: merative-acd-chart
spec:
  ingress:
    - ports:
        - port: 9443
          protocol: TCP
        - port: 9444
          protocol: TCP
  {{- if .Values.networkPolicy.ingress.fromSelectors }}
    {{- with .Values.networkPolicy.ingress.fromSelectors }}
      from:
{{ toYaml . | indent 8 }}
    {{- end }}
  {{- end }}
  podSelector:
    matchLabels:
      acd-ce/serviceType: macroservice
  policyTypes:
    - Ingress
./Kubernetes/merative-acd-ce/crtg/chart/crtg/templates/service.yaml000644 000766 000024 00000001350 14317125246 026211 0ustar00dweberstaff000000 000000 kind: Service
apiVersion: v1
metadata:
  name: merative-acd-crtg
  namespace: {{ .Release.Namespace }}
  labels:
    app.kubernetes.io/name: merative-acd-crtg
    app.kubernetes.io/instance: merative-acd-crtg-{{ .Release.Name }}
    app.kubernetes.io/managed-by: Helm
    app.kubernetes.io/version: "2.0.0"
    helm.sh/chart: merative-acd-chart
    release: v2
  annotations:
    service.kubernetes.io/ibm-load-balancer-cloud-provider-ip-type: private
    service.beta.openshift.io/serving-cert-secret-name: merative-acd-crtg-certs-keystore
spec:
  ports:
  - name: crtg-https-pxy
    protocol: TCP
    port: 443
    targetPort: crtg-https-pxy
  selector:
    app.kubernetes.io/name: merative-acd-crtg
  type: ClusterIP
  sessionAffinity: None
./Kubernetes/merative-acd-ce/crtg/chart/crtg/templates/configmap-nginx-server.yaml000644 000766 000024 00000000257 14317125246 031146 0ustar00dweberstaff000000 000000 apiVersion: v1
kind: ConfigMap
metadata:
  name: nginx-server
  namespace: {{ .Values.namespace }}
data:
  nginx-server.conf: |
{{ .Files.Get "nginx-server.conf" | indent 4}}
./Kubernetes/merative-acd-ce/cdc/chart/000755 000766 000024 00000000000 14422054035 020515 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/cdc/chart/cdc/000755 000766 000024 00000000000 14422054043 021245 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/cdc/chart/cdc/Chart.yaml000644 000766 000024 00000000171 14317125246 023200 0ustar00dweberstaff000000 000000 apiVersion: v2
appVersion: "2.0"
description: A Helm chart for Kubernetes
name: merative-acd-ce-cdc-chart
version: 2.0.0
./Kubernetes/merative-acd-ce/cdc/chart/cdc/templates/000755 000766 000024 00000000000 14422027371 023247 5ustar00dweberstaff000000 000000 ./Kubernetes/merative-acd-ce/cdc/chart/cdc/values.yaml000644 000766 000024 00000001361 14425266727 023452 0ustar00dweberstaff000000 000000 annotations:
  TOOLCHAIN_ID: ""
  GIT_URL: ""
  GIT_BRANCH: ""
  GIT_COMMIT: ""
  USER_NAME: ""
  APPLICATION_VERSION: "" 
configurationStorage:
  backend: file
  sharedPrefix: tenant_data/ibm_supertenant
  tenantPrefix: tenant_data
  s3:
    bucket: ""
    endpointUrl: ""
    location: ""
  file:
    persistent: true
    volume:
      existingClaimName: ""
      supplementalGroup: ""
container:
  image: acdcontaineredition.azurecr.io/acd-ce/concept-dictionary
  digest: 6611c2a1c301e6d9e653df7d4bb12b3113bb409cfc3259c0fb48dcb36fa4d2ac
  tag: "20230504.2122"
replicas: 1
resources:
  limits:
    cpu: ""
    ephemeralStorage: 2Gi
    memory: 14G
  requests:
    cpu: 100m
    ephemeralStorage: 900Mi
    memory: 14G
tenantHeader: ""
tolerations: []
./Kubernetes/merative-acd-ce/cdc/chart/cdc/templates/deployment.yaml000644 000766 000024 00000024743 14422232271 026322 0ustar00dweberstaff000000 000000 kind: Deployment
apiVersion: apps/v1
metadata:
  name: merative-acd-cdc
  namespace: {{ .Release.Namespace }}
  labels:
    app.kubernetes.io/name: merative-acd-cdc
    app.kubernetes.io/instance: merative-acd-cdc-{{ .Release.Name }}
    app.kubernetes.io/managed-by: Helm
    app.kubernetes.io/part-of: merative-acd-ce
    app.kubernetes.io/version: "2.0.0"
    helm.sh/chart: merative-acd-chart
  annotations:
    TOOLCHAIN_ID: "{{ .Values.annotations.TOOLCHAIN_ID }}"
    GIT_URL: "{{ .Values.annotations.GIT_URL }}"
    GIT_BRANCH: "{{ .Values.annotations.GIT_BRANCH }}"
    GIT_COMMIT: "{{ .Values.annotations.GIT_COMMIT }}"
    USER_NAME: "{{ .Values.annotations.USER_NAME }}"
    APPLICATION_VERSION: "{{ .Values.annotations.APPLICATION_VERSION }}"    
spec:
  replicas: {{ .Values.replicas }}
  selector:
    matchLabels:
      app.kubernetes.io/name: merative-acd-cdc
  strategy:
    type: RollingUpdate
    rollingUpdate:
      maxSurge: "25%"
      maxUnavailable: "25%"
  template:
    metadata:
      annotations:
        productID: ""
        productName: ""
        productVersion: 2.0.0
        productMetric: VIRTUAL_PROCESSOR_CORE
        productChargedContainers: ""
      creationTimestamp:
      labels:
        app.kubernetes.io/context: concept_dictionary
        app.kubernetes.io/instance: merative-acd-cdc-{{ .Release.Name }}
        app.kubernetes.io/managed-by: Helm
        app.kubernetes.io/name: merative-acd-cdc
        app.kubernetes.io/part-of: merative-acd-ce
        app.kubernetes.io/version: "2.0.0"
        app.kubernetes.io/versionedApp: merative-acd-cdc-{{ .Values.container.tag }}
        helm.sh/chart: merative-acd-chart
        acd/serviceType: macroservice
    spec:
      hostNetwork: false
      hostPID: false
      hostIPC: false
      imagePullSecrets:
        - name: artifactory.commops.merative.com
      containers:
        - name: merative-acd-cdc
          image: {{ .Values.container.image }}@sha256:{{ .Values.container.digest }}
          env:
            - name: "clinical_data_annotator_artifactstore_shared_backend"
              value: "{{ .Values.configurationStorage.backend }}"
            - name: "clinical_data_annotator_artifactstore_tenant_backend"
              value: "{{ .Values.configurationStorage.backend }}"
            - name: "clinical_data_annotator_artifactstore_tenant_prefix"
              value: "{{ .Values.configurationStorage.tenantPrefix }}"
            - name: "clinical_data_annotator_artifactstore_shared_prefix"
              value: "{{ .Values.configurationStorage.sharedPrefix }}"
            - name: "clinical_data_annotator_artifactstore_cos_buckets"
              value: "{{ .Values.configurationStorage.s3.bucket }}"
            - name: "clinical_data_annotator_artifactstore_cos_tenants"
              value: "wh-acd"
            - name: "clinical_data_annotator_artifactstore_cos_accessKeyIdFiles"
              value: "ibm_wh_acd_as/username"
            - name: "clinical_data_annotator_artifactstore_cos_accessKeySecretFiles"
              value: "ibm_wh_acd_as/password"
            - name: "clinical_data_annotator_artifactstore_cos_endpointUrl"
              value: "{{ .Values.configurationStorage.s3.endpointUrl }}"
            - name: "clinical_data_annotator_artifactstore_cos_location"
              value: "{{ .Values.configurationStorage.s3.location }}"
            - name: "clinical_data_annotator_common_client_auth_enabled"
              value: "false"
            - name: "clinical_data_annotator_common_concurrent_blocking_threshold"
              value: "10"
            - name: "clinical_data_annotator_common_concurrent_reject_threshold"
              value: "50"
            - name: "clinical_data_annotator_common_concurrent_uri_pattern_list"
              value: "/v1/concept_dictionary.*"
            - name: "clinical_data_annotator_common_context_root"
              value: "services/concept_dictionary"
            - name: "clinical_data_annotator_common_enabled_dark_features"
              value: "{{ .Values.enabledDarkFeatures }}"
            - name: "clinical_data_annotator_common_http_port"
              value: "-1"
            - name: "clinical_data_annotator_common_https_port"
              value: "9443"
            - name: "clinical_data_annotator_common_log_event_format"
              value: "json"
            - name: "clinical_data_annotator_common_max_heap"
              value: "12G"
            - name: "clinical_data_annotator_common_min_heap"
              value: "12G"
            - name: "clinical_data_annotator_common_service_name"
              value: "concept-dictionary"
            - name: "clinical_data_annotator_common_shared_config_dir"
              value: "/opt/ibm/watsonhealth/services/config"
            {{- if .Values.tenantHeader }}
            - name: "clinical_data_annotator_services_authentication_type"
              value: "custom_header"
            - name: "clinical_data_annotator_services_authentication_header"
              value: "{{ .Values.tenantHeader }}"
            {{- end }}
          terminationMessagePath: /dev/termination-log
          terminationMessagePolicy: File
          imagePullPolicy: IfNotPresent
          ports:
            - name: cdc-https
              containerPort: 9443
              protocol: TCP
          volumeMounts:
            - name: as-volume
              mountPath: /opt/ibm/watsonhealth/services/config/secrets/ibm_wh_acd_as
              readOnly: true
            - name: certs-keystore-volume
              mountPath: /tmp/keystore
              readOnly: true
            - name: certs-truststore-volume
              mountPath: /opt/ibm/watsonhealth/services/config/certs/truststore
              readOnly: true
            - name: configmap-env-volume
              mountPath: /opt/ibm/watsonhealth/services/config/configmaps
              readOnly: true
          {{- if and (eq .Values.configurationStorage.backend "file") .Values.configurationStorage.file.persistent }}
            - name: {{ .Release.Name }}-file-store-pvc
              mountPath: /opt/ibm/watsonhealth/services/config/artifactstore/tenant_data
              readOnly: false
          {{- end }}
          startupProbe:
            exec:
              command:
                - /staging/whcs-devops-ucd/docker/k8s_startup.sh
            initialDelaySeconds: 30
            timeoutSeconds: 1800
            periodSeconds: 30
            successThreshold: 1
            failureThreshold: 10
          livenessProbe:
            exec:
              command:
                - /staging/whcs-devops-ucd/docker/docker_liveness.sh
            initialDelaySeconds: 5
            periodSeconds: 30
            timeoutSeconds: 10
            failureThreshold: 5
          readinessProbe:
            exec:
              command:
                - /staging/whcs-devops-ucd/docker/docker_readiness.sh
            initialDelaySeconds: 5
            periodSeconds: 60
            timeoutSeconds: 10
            failureThreshold: 1
          resources:
            requests:
              cpu: {{ index .Values.resources.requests.cpu}}
              ephemeral-storage: {{ index .Values.resources.requests "ephemeralStorage" }}
              memory: {{ .Values.resources.requests.memory }}
            limits:
              ephemeral-storage: {{ index .Values.resources.limits "ephemeralStorage" }}
              memory: {{ .Values.resources.limits.memory }}
          securityContext:
            privileged: false
            readOnlyRootFilesystem: false
            allowPrivilegeEscalation: false
            runAsNonRoot: true
          {{- if not (.Capabilities.APIVersions.Has "security.openshift.io/v1") }}
            runAsUser: 1001
          {{- end }}
            capabilities:
              drop: ["ALL"]
      securityContext:
        runAsNonRoot: true
      {{- if not (.Capabilities.APIVersions.Has "security.openshift.io/v1") }}
        runAsUser: 1001
      {{- end }}
      {{- if eq .Values.configurationStorage.backend "file" }}
        {{- if .Values.configurationStorage.file.volume.supplementalGroup }}
        supplementalGroups: [{{ .Values.configurationStorage.file.volume.supplementalGroup }}]
        {{- end }}
      {{- end }}
      volumes:
      - name: as-volume
        secret:
          secretName: merative-acd-as
          optional: true
      - name: certs-keystore-volume
        secret:
          secretName: merative-acd-cdc-certs-keystore
        {{- if not (.Capabilities.APIVersions.Has "security.openshift.io/v1") }}
          optional: true
        {{- end }}
      - name: certs-truststore-volume
        configMap:
          name: merative-acd-ce-certs-truststore-pem
          optional: true
      - name: configmap-env-volume
        configMap:
          name: merative-acd-custom-env
          optional: true
      - name: {{ .Release.Name }}-file-store-pvc
      {{- if and (eq .Values.configurationStorage.backend "file") .Values.configurationStorage.file.persistent }}
        persistentVolumeClaim:
        {{- if .Values.configurationStorage.file.volume.existingClaimName }}
          claimName: {{ .Values.configurationStorage.file.volume.existingClaimName }}
        {{- else }}
          claimName: {{ .Release.Name }}-file-store-pvc
        {{- end }}
      {{- else }}
        emptyDir: {}
      {{- end }}
      affinity:
        nodeAffinity:
          requiredDuringSchedulingIgnoredDuringExecution:
            nodeSelectorTerms:
              - matchExpressions:
                - key: kubernetes.io/arch
                  operator: In
                  values:
                    - amd64
        podAntiAffinity:
          preferredDuringSchedulingIgnoredDuringExecution:
          - podAffinityTerm:
              labelSelector:
                matchExpressions:
                - key: app.kubernetes.io/versionedApp
                  operator: In
                  values:
                  - merative-acd-cdc-{{ .Values.container.tag }}
              topologyKey: failure-domain.alpha.kubernetes.io/zone
            weight: 100
          requiredDuringSchedulingIgnoredDuringExecution:
          - labelSelector:
              matchExpressions:
              - key: app.kubernetes.io/versionedApp
                operator: In
                values:
                - merative-acd-cdc-{{ .Values.container.tag }}
            topologyKey: kubernetes.io/hostname
    {{- with .Values.tolerations }}
      tolerations:
{{ toYaml . | indent 8 }}
    {{- end }}
      restartPolicy: Always
      terminationGracePeriodSeconds: 30
      dnsPolicy: ClusterFirst
      dnsConfig:
        options:
          - name: single-request
      schedulerName: default-scheduler
./Kubernetes/merative-acd-ce/cdc/chart/cdc/templates/service.yaml000644 000766 000024 00000001324 14317125246 025576 0ustar00dweberstaff000000 000000 kind: Service
apiVersion: v1
metadata:
  name: merative-acd-cdc
  namespace: {{ .Release.Namespace }}
  labels:
    app.kubernetes.io/name: merative-acd-cdc
    app.kubernetes.io/instance: merative-acd-cdc-{{ .Release.Name }}
    app.kubernetes.io/managed-by: Helm
    app.kubernetes.io/version: "2.0.0"
    helm.sh/chart: merative-acd-chart
    release: v2
  annotations:
    service.kubernetes.io/ibm-load-balancer-cloud-provider-ip-type: private
    service.beta.openshift.io/serving-cert-secret-name: merative-acd-cdc-certs-keystore
spec:
  ports:
  - name: cdc-https
    protocol: TCP
    port: 443
    targetPort: 9443
  selector:
    app.kubernetes.io/name: merative-acd-cdc
  type: ClusterIP
  sessionAffinity: None
./Kubernetes/merative-acd-ce/cdc/chart/cdc/templates/configmap-ca.yaml000644 000766 000024 00000001237 14317125246 026465 0ustar00dweberstaff000000 000000 {{- if (.Capabilities.APIVersions.Has "security.openshift.io/v1") }}
apiVersion: v1
metadata:
  name: merative-acd-ce-certs-truststore-pem
  namespace: {{ .Release.Namespace }}
  annotations:
    meta.helm.sh/release-name: {{ .Release.Name }}
    meta.helm.sh/release-namespace: {{ .Release.Namespace }}
    service.beta.openshift.io/inject-cabundle: "true"
  labels:
    app.kubernetes.io/name: merative-acd-ce-certs-truststore-pem
    app.kubernetes.io/instance: merative-acd-ce-certs-truststore-pem-{{ .Release.Name }}
    helm.sh/chart: merative-acd-chart
    app.kubernetes.io/managed-by: Helm
    app.kubernetes.io/version: "2.0.0"
data:
kind: ConfigMap
{{- end }}
./Docker/acd-ce-images.txt000755 000766 000024 00000000712 14425267026 016171 0ustar00dweberstaff000000 000000 # list of images to pull and/or load
clinical-data-annotator:20230504.1750
advanced-care-insights:20230504.2122
attribute-detection:20230504.2122
concept-detection:20230504.2122
concept-disambiguation:20230504.2122
concept-value-detection:20230504.2122
hypothetical-detection:20230504.2122
model-broker:20230504.2122
negation-detection:20230504.2122
ontology:20230504.2122
spell-checker:20230504.2122
cartridge:20230504.1750
concept-dictionary:20230504.2122
./Docker/docker_deploy_service.sh000755 000766 000024 00000062576 14427161214 017762 0ustar00dweberstaff000000 000000 #!/bin/bash
# ***************************************************************** 
#                                                                   
# Merative Confidential                                             
#                                                                   
# (C) Copyright Merative US L.P. 2001, 2023 
#                                                                   
# ***************************************************************** 

echo "####################"
echo "Executing $SCRIPT_NAME"
if [ -e "$(dirname "$0")/../service" ]; then
  SERVICE_SCRIPT_DIR="$(cd "$(dirname "$0")/../service"; pwd -P)"
else
  SERVICE_SCRIPT_DIR="$(cd "$(dirname "$0")"; pwd -P)"
fi

#########################################################################
#Global vars
#########################################################################
retries_max=120
UNAME="$(uname -s)"

#########################################################################
#Common functions
#########################################################################
print_help() {
  echo "Options:"
  echo "  -action ${action}                                     (start|stop) Start or stop the service."
  echo "  -environment_properties <environment_properties>  Environment properties. For deploying single environment containing multiple services. Mutually exclusive with -service_properties."
  echo "  -image_list <image-list-file> Optional file to be used with env props to override versions per service."
  echo "  -help|-h                                          Script help."
  echo "  -iam_apikey <iam_apikey>                          IAM apikey for accessing image registry."
  echo "  -pull_image ${pull_image}                                 (true|false|refresh) Pull image from repository.  Refresh forces refresh of local repository."
  echo "  -registry <registry>                              image registy"
  echo "  -registry_namespace <registry_namespace>          Image registry namespace."
  echo "  -service_properties <service_properties>          Service properties. For deploying single service. Mutually exclusive with -environment_properties."
  echo "  -service_name <service_name>                      Service name for deploying."
  echo "  -service_version ${service_version}                           Service version for deploying."
  echo "  -store_password <store_password>                  Keystore and truststore password. Needed if generating these or inserting certificates as part of the deployment."

  echo "Usage:"
  echo "  $SCRIPT_NAME [options]"

  echo "Examples:"
  echo "  # Deploy all the services for an environment"
  echo "  $SCRIPT_NAME -environment_properties det.properties"
  echo "  # Deploy a specific service"
  echo "  $SCRIPT_NAME -service_name clinical-data-annotator -service_properties clinical-data-annotator.properties -service_version 20190401.0100"
}

generate_jks() {
  if [ ! -z "${com_ibm_watson_health_common_shared_config_dir}" ]; then
    mkdir -p ${com_ibm_watson_health_common_shared_config_dir}
    chmod -f 777 ${com_ibm_watson_health_common_shared_config_dir}
  elif [ ! -z "${clinical_data_annotator_common_shared_config_dir}" ]; then
    mkdir -p ${clinical_data_annotator_common_shared_config_dir}
    chmod -f 777 ${clinical_data_annotator_common_shared_config_dir}
  fi
  if [ ! -e "${com_ibm_watson_health_common_shared_config_dir}/keystore/key.jks" ]; then
    if [ -z "${store_password}" ]; then
      echo "Keystore parameter not provided"
      return 1;
    fi
    storeType=jks
    # openjdk uses a different certs setup
    if [[ -f /usr/lib/jvm/jre/lib/security/cacerts ]]; then
      storeType=pkcs12
    fi
    mkdir -p ${com_ibm_watson_health_common_shared_config_dir}/keystore
    keytool -genkey \
          -alias 'wh-int' \
          -keyalg RSA \
          -keypass "${store_password}" \
          -keysize 2048 \
          -dname "O=ibm.com,OU=Watson Health" \
          -keystore "${com_ibm_watson_health_common_shared_config_dir}/keystore/key.jks" \
          -storepass "${store_password}" \
          -storetype ${storeType}
    if [ $? != 0 ]; then
      echo "Create keystore failed"
      return 1;
    fi
    mkdir -p ${com_ibm_watson_health_common_shared_config_dir}/certs
    keytool -exportcert \
            -keystore "${com_ibm_watson_health_common_shared_config_dir}/keystore/key.jks" \
            -storepass "${store_password}" \
            -alias 'wh-int' \
            -file "${com_ibm_watson_health_common_shared_config_dir}"/certs/wh-int.crt \
            -rfc
    if [ $? != 0 ]; then
      echo "Create certificate failed"
      return 1;
    fi

    if [ ! -e "${com_ibm_watson_health_common_shared_config_dir}/truststore/trust.jks" ]; then
      if [ -z "${store_password}" ]; then
        echo "Keystore parameter not provided"
        return 1;
      fi
      mkdir -p ${com_ibm_watson_health_common_shared_config_dir}/truststore
      keytool -import \
          -keystore "${com_ibm_watson_health_common_shared_config_dir}/truststore/trust.jks" \
          -storepass "${store_password}" \
          -alias 'wh-int' \
          -file "${com_ibm_watson_health_common_shared_config_dir}"/certs/wh-int.crt \
          -noprompt
      if [ $? != 0 ]; then
        echo "importing of cert into truststore failed"
        return 1;
      fi
    fi
    # add .p12 version of client key under certs dir to make service_configure.sh in images
    # pick that up vs generating its own wh-int key in Keystore
    if [ ! -e "${com_ibm_watson_health_common_shared_config_dir}/certs/keystore/wh-int.p12" ]; then
      if [ -z "${store_password}" ]; then
        echo "Keystore parameter not provided"
        return 1;
      fi
      mkdir -p ${com_ibm_watson_health_common_shared_config_dir}/certs/keystore
      keytool -importkeystore \
            -srckeystore "${com_ibm_watson_health_common_shared_config_dir}/keystore/key.jks" \
            -srcstorepass "${store_password}" \
            -srcstoretype pkcs12 \
            -alias 'wh-int' \
            -destkeystore "${com_ibm_watson_health_common_shared_config_dir}"/certs/keystore/wh-int.p12 \
            -deststorepass "${store_password}" \
            -deststoretype pkcs12 \
            -noprompt
      if [ $? != 0 ]; then
        echo "exporting cert to p12 file failed"
        return 1;
      fi
    fi
  elif [ ! -e "${clinical_data_annotator_common_shared_config_dir}/keystore/key.jks" ]; then
    if [ -z "${store_password}" ]; then
      echo "Keystore parameter not provided"
      return 1;
    fi
    storeType=jks
    # openjdk uses a different certs setup
    if [[ -f /usr/lib/jvm/jre/lib/security/cacerts ]]; then
      storeType=pkcs12
    fi
    mkdir -p ${clinical_data_annotator_common_shared_config_dir}/keystore
    keytool -genkey \
          -alias 'wh-int' \
          -keyalg RSA \
          -keypass "${store_password}" \
          -keysize 2048 \
          -dname "O=ibm.com,OU=Watson Health" \
          -keystore "${clinical_data_annotator_common_shared_config_dir}/keystore/key.jks" \
          -storepass "${store_password}" \
          -storetype ${storeType}
    if [ $? != 0 ]; then
      echo "Create keystore failed"
      return 1;
    fi
    mkdir -p ${clinical_data_annotator_common_shared_config_dir}/certs
    keytool -exportcert \
            -keystore "${clinical_data_annotator_common_shared_config_dir}/keystore/key.jks" \
            -storepass "${store_password}" \
            -alias 'wh-int' \
            -file "${clinical_data_annotator_common_shared_config_dir}"/certs/wh-int.crt \
            -rfc
    if [ $? != 0 ]; then
      echo "Create certificate failed"
      return 1;
    fi

    if [ ! -e "${clinical_data_annotator_common_shared_config_dir}/truststore/trust.jks" ]; then
      if [ -z "${store_password}" ]; then
        echo "Keystore parameter not provided"
        return 1;
      fi
      mkdir -p ${clinical_data_annotator_common_shared_config_dir}/truststore
      keytool -import \
          -keystore "${clinical_data_annotator_common_shared_config_dir}/truststore/trust.jks" \
          -storepass "${store_password}" \
          -alias 'wh-int' \
          -file "${clinical_data_annotatorh_common_shared_config_dir}"/certs/wh-int.crt \
          -noprompt
      if [ $? != 0 ]; then
        echo "importing of cert into truststore failed"
        return 1;
      fi
    fi
    # add .p12 version of client key under certs dir to make service_configure.sh in images
    # pick that up vs generating its own wh-int key in Keystore
    if [ ! -e "${clinical_data_annotator_common_shared_config_dir}/certs/keystore/wh-int.p12" ]; then
      if [ -z "${store_password}" ]; then
        echo "Keystore parameter not provided"
        return 1;
      fi
      mkdir -p ${clinical_data_annotator_common_shared_config_dir}/certs/keystore
      keytool -importkeystore \
            -srckeystore "${clinical_data_annotator_common_shared_config_dir}/keystore/key.jks" \
            -srcstorepass "${store_password}" \
            -srcstoretype pkcs12 \
            -alias 'wh-int' \
            -destkeystore "${clinical_data_annotator_common_shared_config_dir}"/certs/keystore/wh-int.p12 \
            -deststorepass "${store_password}" \
            -deststoretype pkcs12 \
            -noprompt
      if [ $? != 0 ]; then
        echo "exporting cert to p12 file failed"
        return 1;
      fi
    fi
  fi
}

stop_service() {
  local service_name=$1
  local runtime_properties=$2

  if [ -z "${runtime_properties}" ] || [ ! -e "${runtime_properties}" ]; then
    echo "Runtime properties not found"
    return 1
  fi
  . ${runtime_properties}
  if [ ! -z "${com_ibm_watson_health_common_service_name}" ]; then
    container_name="${com_ibm_watson_health_common_service_name}"
  elif [ ! -z "${clinical_data_annotator_common_service_name}" ]; then
    container_name="${clinical_data_annotator_common_service_name}"
  else
    container_name="${service_name}"
  fi

  container_info=$(docker container inspect ${container_name} 2>&1)
  if [[ "${container_info}" != *"No such container"* ]]; then
    echo "Stopping container ${container_name}"
    docker stop ${container_name} 1>/dev/null
    if [ $? != 0 ]; then
      echo "docker stop failed"
      return 1;
    fi
    docker wait ${container_name} 1>/dev/null
    if [ $? != 0 ]; then
      echo "docker wait failed"
      return 1;
    fi
    docker rm ${container_name} 1>/dev/null
    if [ $? != 0 ]; then
      echo "docker rm failed"
      return 1;
    fi
    echo "Stopping successful"
  fi
}

start_service() {
  local service_name=$1
  local service_version=$2
  local runtime_properties=$3

  if [ -z "${runtime_properties}" ] || [ ! -e "${runtime_properties}" ]; then
    echo "Runtime properties not found"
    return 1
  fi
  . ${runtime_properties}
  if [ ! -z "${com_ibm_watson_health_common_service_name}" ]; then
    container_name="${com_ibm_watson_health_common_service_name}"
  elif [ ! -z "${clinical_data_annotator_common_service_name}" ]; then
    container_name="${clinical_data_annotator_common_service_name}"
  else
    container_name="${service_name}"
  fi

  if [ -z "${store_password}" ]; then
    sed -i'' "s#\(STORE_PWD=\).*\$#\1${store_password}#" ${micro_service_runtime_properties}
  fi

  # Generate keystore
  if [ ! -z "${com_ibm_watson_health_common_shared_config_dir}" ]; then
    generate_jks
    if [ $? != 0 ]; then
      return 1;
    fi
  fi

  echo "Starting container ${container_name}, version ${service_version}"

  # Setup shared file system
  local docker_volumes=
  if [ ! -z "${com_ibm_watson_health_common_docker_volume}" ]; then
    IFS=',' read -r -a docker_volume_array <<< "${com_ibm_watson_health_common_docker_volume}"
    for docker_volume in "${docker_volume_array[@]}"; do
      docker_volumes="${docker_volumes} -v ${docker_volume}"
    done
  elif [ ! -z "${clinical_data_annotator_common_docker_volume}" ]; then
      IFS=',' read -r -a docker_volume_array <<< "${clinical_data_annotator_common_docker_volume}"
    for docker_volume in "${docker_volume_array[@]}"; do
      docker_volumes="${docker_volumes} -v ${docker_volume}"
    done
  fi

  # Setup user mapping
  local docker_user=
  if [ ! -z "${com_ibm_watson_health_common_docker_user}" ]; then
    docker_user="-u ${com_ibm_watson_health_common_docker_user}"
  elif [ ! -z "${clinical_data_annotator_common_docker_user}" ]; then
    docker_user="-u ${clinical_data_annotator_common_docker_user}"
  fi

  local docker_group_add=
  if [ ! -z "${com_ibm_watson_health_common_docker_group_add}" ]; then
    docker_group_add="--group-add ${com_ibm_watson_health_common_docker_group_add}"
    # Hack for RDT until file permissions are set correctly
    if [ ${com_ibm_watson_health_common_docker_group_add} == "30000" ]; then
      docker_group_add="${docker_group_add} --group-add 31001"
    fi
  elif [ ! -z "${clinical_data_annotator_common_docker_group_add}" ]; then
    docker_group_add="--group-add ${clinical_data_annotator_common_docker_group_add}"
    # Hack for RDT until file permissions are set correctly
    if [ ${clinical_data_annotator_common_docker_group_add} == "30000" ]; then
      docker_group_add="${docker_group_add} --group-add 31001"
    fi
  fi

  # Specify shared memory
  docker_shared_memory_size=
  if [ ! -z "${com_ibm_watson_health_common_docker_shared_memory_size}" ]; then
    docker_shared_memory_size="--shm-size=${com_ibm_watson_health_common_docker_shared_memory_size}"
  elif [ ! -z "${clinical_data_annotator_common_docker_shared_memory_size}" ]; then
    docker_shared_memory_size="--shm-size=${clinical_data_annotator_common_docker_shared_memory_size}"
  fi

  # Create bridge for service communications
  docker_networks=$(docker network ls)
  if [[ "${docker_networks}" != *"service_bridge"* ]]; then
    docker network create service_bridge
    if [ $? != 0 ]; then
      echo "docker network create service_bridge failed"
      return 1;
    fi
  fi

  docker_port_mappings=
  if [ ! -z "${com_ibm_watson_health_common_http_port}" ] && [ "${com_ibm_watson_health_common_http_port}" != "-1" ]; then
    docker_port_mappings="-p ${com_ibm_watson_health_common_http_port}:9080"
  elif [ ! -z "${clinical_data_annotator_common_http_port}" ] && [ "${clinical_data_annotator_common_http_port}" != "-1" ]; then
    docker_port_mappings="-p ${clinical_data_annotator_common_http_port}:9080"
  fi
  if [ ! -z "${com_ibm_watson_health_common_https_port}" ] && [ "${com_ibm_watson_health_common_https_port}" != "-1" ]; then
    docker_port_mappings="${docker_port_mappings} -p ${com_ibm_watson_health_common_https_port}:9443"
  elif [ ! -z "${clinical_data_annotator_common_https_port}" ] && [ "${clinical_data_annotator_common_https_port}" != "-1" ]; then
    docker_port_mappings="-p ${clinical_data_annotator_common_https_port}:9443"
  fi

  # Display runtime properties
  echo "runtime_properties=${runtime_properties}"

  # Always clear out any dangling images to help with storage
  docker rmi $(docker images -f "dangling=true" -q) 2>/dev/null

  # Refresh image
  image_name=${registry}/${registry_namespace}/${service_name}
  if [ "${pull_image}" == "refresh" ]; then
    echo "Removing old ${image_name} images"
    docker rmi $(docker images ${image_name} -q) -f > /dev/null 2>&1
  fi
  if [ "${pull_image}" != "false" ]; then
    docker pull ${image_name}:${service_version}
    if [ $? != 0 ]; then
      echo "docker pull ${image_name}:${service_version} failed"
      return 1;
    fi
  fi

  # Start container
  echo "docker run --restart always --env-file ${runtime_properties} --name ${container_name} ${docker_port_mappings} ${docker_volumes} ${docker_shared_memory_size} ${docker_user} ${docker_group_add} -t ${image_name}:${service_version} > $(hostname -s)_${container_name}.log"
  docker run --restart always \
             --env-file ${runtime_properties} \
             --name ${container_name} \
             ${docker_port_mappings} \
             ${docker_volumes} \
             ${docker_shared_memory_size} \
             ${docker_user} \
             ${docker_group_add} \
             -t ${image_name}:${service_version} \
             > $(hostname -s)_${container_name}.log &
  if [ $? != 0 ]; then
    echo "docker run --name ${container_name} failed"
    return 1;
  fi

  # Wait for container to be in running state
  retries=0
  until [ "$(docker inspect ${container_name} -f {{.State.Running}} 2>/dev/null)" == "true" ] || (( retries++ >= retries_max )); do
    sleep 1m
  done
  if [ "${retries}" -gt "${retries_max}" ]; then
    echo "Container failed to enter running state"
    return 1
  fi

  # Connect service to bridge
  docker network connect service_bridge ${container_name}
  if [ $? != 0 ]; then
    echo "docker network connect service_bridge"
    return 1;
  fi
  cur_dir=$(pwd)
  echo "Starting successful. Logs can be found in: ${cur_dir}/${container_name}.log"
}

start_or_restart_service() {
  local service_name=$1
  local service_version=$2
  local runtime_properties=$3

  stop_service "${service_name}" "${runtime_properties}"
  if [ $? != 0 ]; then
    return 1;
  fi
  start_service "${service_name}" "${service_version}" "${runtime_properties}"
  if [ $? != 0 ]; then
    return 1;
  fi
}

# Need to merge into mainline
start_or_restart_macro_service() {
  local service_name=$1
  local service_version=$2
  local macro_service_runtime_properties=$3

  . ${macro_service_runtime_properties}

  # Restart micro services
#  while IFS= read -r env_var ; do
#    env_var_name=$(echo $env_var | cut -f1 -d=)
#    if [[ ${env_var_name} == 'MICRO_SERVICE_'*'_ENABLE' ]]; then
#      micro_service_name_upper=$(echo $env_var_name | sed "s#=.*##" | sed "s#MICRO_SERVICE_##" | sed "s#_ENABLE##")
#      micro_service_name=$(echo "${micro_service_name_upper}" | perl -ne 'print lc' | tr '_' '-')
#      echo "Processing micro service ${micro_service_name}"
#      micro_service_enabled=$(echo $env_var | cut -f2- -d=)
#      echo "Micro service enabled: ${micro_service_enabled}"
#      micro_service_http_port_variable="MICRO_SERVICE_${micro_service_name_upper}_com_ibm_watson_health_common_http_port"
#      micro_service_http_port=${!micro_service_http_port_variable}
#      micro_service_https_port_variable="MICRO_SERVICE_${micro_service_name_upper}_HTTPS_PORT"
#      micro_service_https_port=${!micro_service_https_port_variable}
#      micro_service_context_root=$(echo "${micro_service_name_upper}" | perl -ne 'print lc')
#      micro_service_url="https://${micro_service_name}:9443/services/${micro_service_context_root}"
#      echo "Micro service url: ${micro_service_url}"
#      if [ "${micro_service_enabled}" == "true" ]; then
#        micro_service_runtime_properties="${macro_service_runtime_properties}_micro"
#        cp "${macro_service_runtime_properties}" "${micro_service_runtime_properties}"
#        echo "MICRO_SERVICE_${micro_service_name_upper}_URL=${micro_service_url}" >> ${macro_service_runtime_properties}
#        if [[ $UNAME == Darwin* ]]; then
#          sed -i '' "s#\(com_ibm_watson_health_common_http_port=\).*\$#\1${micro_service_http_port}#" ${micro_service_runtime_properties}
#          sed -i '' "s#\(com_ibm_watson_health_common_https_port=\).*\$#\1${micro_service_https_port}#" ${micro_service_runtime_properties}
#        else
#          sed -i'' "s#\(com_ibm_watson_health_common_http_port=\).*\$#\1${micro_service_http_port}#" ${micro_service_runtime_properties}
#          sed -i'' "s#\(com_ibm_watson_health_common_https_port=\).*\$#\1${micro_service_https_port}#" ${micro_service_runtime_properties}
#        fi
#        cat "${micro_service_runtime_properties}"
#        start_or_restart_service "${micro_service_name}" "${service_version}" "${micro_service_runtime_properties}"
#        if [ $? != 0 ]; then
#          rm -f "${micro_service_runtime_properties}"
#          return 1;
#        fi
#        rm -f "${micro_service_runtime_properties}"
#      fi
#    fi
#  done < <(set)

  # Start or restart macro service
  cat "${macro_service_runtime_properties}"
  start_or_restart_service "${service_name}" "${service_version}" "${macro_service_runtime_properties}"
  if [ $? != 0 ]; then
    return 1;
  fi
}

# Need to merge into mainline
stop_macro_service() {
  local service_name=$1
  local macro_service_runtime_properties=$2

  # Stop macro service
  stop_service "${service_name}" "${macro_service_runtime_properties}"
  if [ $? != 0 ]; then
    return 1;
  fi

  # Restart micro services
#  while IFS= read -r env_var ; do
#    env_var_name=$(echo $env_var | cut -f1 -d=)
#    if [[ ${env_var_name} == 'MICRO_SERVICE_'*'_ENABLE' ]]; then
#      micro_service_name_upper=$(echo $env_var_name | sed "s#=.*##" | sed "s#MICRO_SERVICE_##" | sed "s#_ENABLE##")
#      micro_service_name=$(echo "${micro_service_name_upper}" | perl -ne 'print lc' | tr '_' '-')
#      echo "Processing micro service ${micro_service_name}"
#      micro_service_enabled=$(echo $env_var | cut -f2- -d=)
#      echo "Micro service enabled: ${micro_service_enabled}"
#      if [ "${micro_service_enabled}" == "true" ]; then
#        stop_service "${micro_service_name}" "${micro_service_runtime_properties}"
#        if [ $? != 0 ]; then
#          return 1;
#        fi
#      fi
#    fi
#  done < <(set)
}

#########################################################################
#Parameter management
#########################################################################
#Parameter defaults
action=start
environment_properties=
image_file_list=
iam_apikey=
pull_image=false
registry=us.icr.io
registry_namespace=
service_properties=
service_name=
service_version="latest"

while [[ $# -gt 0 ]]
do
  key="$1"
  case $key in
    -action)
      action="$2"
      echo "action=${action}"
      shift
      ;;
    -environment_properties)
      environment_properties="$2"
      echo "environment_properties=${environment_properties}"
      shift
      ;;
    -image_list)
      image_file_list="$2"
      echo "image_file_list=${image_file_list}"
      shift
      ;;
    -help|-h)
      helpRequest=true
      print_help
      exit 0
      shift
      ;;
    -iam_apikey)
      iam_apikey="$2"
      echo "iam_apikey=${iam_apikey}"
      shift
      ;;
    -pull_image)
      pull_image="$2"
      echo "pull_image=${pull_image}"
      shift
      ;;
    -registry)
      registry="$2"
      echo "registry=${registry}"
      shift
      ;;
    -registry_namespace)
      registry_namespace="$2"
      echo "registry_namespace=${registry_namespace}"
      shift
      ;;
    -service_properties)
      service_properties="$2"
      echo "service_properties=${service_properties}"
      shift
      ;;
    -service_name)
      service_name="$2"
      echo "service_name=${service_name}"
      shift
      ;;
    -service_version)
      service_version="$2"
      echo "service_version=${service_version}"
      shift
      ;;
    -store_password)
      store_password="$2"
      echo "store_password=${store_password}"
      shift
      ;;

    *)
      echo "Unknown parameter $1"
  esac
  shift
done

# Parameters checking
if [ ! -z "${environment_properties}" ] && [ ! -z "${service_properties}" ]; then
  echo "Either an environment or service must be deployed"
  exit 1;
fi

#########################################################################
#Mainline
#########################################################################
if [ ! -z "${iam_apikey}" ]; then
  docker login -u iamapikey -p "${iam_apikey}" "${registry}"
fi

if [ ! -z "${service_properties}" ]; then
  case "${action}" in
    start)
      start_or_restart_macro_service "${service_name}" "${service_version}" "${service_properties}"
      ;;
    *)
      stop_macro_service "${service_name}" "${service_properties}"
      ;;
  esac
else
  while IFS= read -r env_var ; do
    env_var_name=$(echo $env_var | cut -f1 -d=)
    if [[ ${env_var_name} == 'BUILD_NAME_'* ]]; then
      env_var_value=$(echo $env_var | cut -f2- -d=)
      env_service_name=$(echo $env_var_value | sed "s#_Service_Build##" | perl -ne 'print lc' | tr '_' '-')
      if [ -z "${service_name}" ] || [ "${env_service_name}" == "${service_name}" ]; then
        echo "Processing service: ${env_service_name}"
        env_service_version=${service_version}
        if [ ! -z "${image_file_list}" ]; then
          # echo "Processing image list file ${image_file_list}"
          match_pattern="${env_service_name}:"
          echo ${match_pattern}
          # find if we have a version to override.
          while IFS= read -r image_name ; do
            # echo "Processing image file entry: ${image_name}"
            if [[ ${image_name} == ${match_pattern}* ]]; then
              env_service_version=$(echo "${image_name}" | sed "s#${env_service_name}:##")
              echo "...with service version: ${env_service_version}"
              break
            fi
          done < ${image_file_list}
        else
          echo "NO image list file provided - using latest for all images"
        fi
        service_properties_no_extension=$(echo "${environment_properties}" | sed "s#.properties##")
        comp_name=$(echo "WHCS_${env_var_value}" | sed "s#_Build##")
        ${SERVICE_SCRIPT_DIR}/service_generate_effective_properties.sh \
           -component_name "${comp_name}" \
           -env_props "${service_properties_no_extension}" \
           -stage "runtime"
        if [ $? != 0 ]; then
          echo "Generate service properties failed."
          exit 1;
        fi
        case "${action}" in
          start)
            start_or_restart_service "${env_service_name}" "${env_service_version}" "runtime_effective.properties"
            ;;
          *)
            stop_service "${env_service_name}" "runtime_effective.properties"
            ;;
        esac
        rm -f runtime_effective.properties
      fi
    fi
  done < ${environment_properties}
fi
./Docker/run-acd-ce.sh000755 000766 000024 00000014315 14422360626 015324 0ustar00dweberstaff000000 000000 #!/bin/bash
# ***************************************************************** 
#                                                                   
# Merative Confidential                                             
#                                                                   
# (C) Copyright Merative US L.P. 2012, 2023 
#                                                                   
# ***************************************************************** 

#########################################################################
#Global vars
#########################################################################
SCRIPT_NAME=$(basename -- "$0")
registry="acdcontaineredition.azurecr.io"
registry_namespace="acd-ce"
label="latest"
IMAGE_FILE_LIST=acd-ce-images.txt
remove=true

UNAME="$(uname -s)"


echo "####################"
echo "Executing $SCRIPT_NAME"

#########################################################################
#Common functions
#########################################################################
print_help() {
  echo "$SCRIPT_NAME Loads the Annotator for Clinical Data Configuration editory into a local docker repo and runs it."
  echo " by default it will stop all running containers, clear the images and reload the images from the latest source files and then start new containers."
  echo "Usage: $SCRIPT_NAME [options...]"
  echo "Options:"
  echo "  -restart  Restarts the containers with the latest configuration data without reloading the images from their source. Use this if you changed the properties file for configuration."
  echo "  -stop    Stops all containers running on the system and don't restart them."
  echo "  -remove  Stops all containers and removes all images and doesn't restart them."
  echo "  -env-props FILE environment properties file to use. Default is acd-ce.properties"
  echo "  -image-list FILE  file to use that has list of images.  Default is $IMAGE_FILE_LIST"
  echo "  -registry <registry> The container registry service to use."
  echo "  -registry_namespace <namespace>  The namespace to use in the registry."
}


load_image() {
  local image_file=$1

  docker load < ${image_file} # 1>/dev/null
  if [ $? != 0 ]; then
    echo "docker load \< ${image_file} failed"
    return 1;
  fi
  return 0;
}



#########################################################################
#Parameter management
#########################################################################
#Parameter defaults
image_file_list=$IMAGE_FILE_LIST
env_properties=acd-ce.properties
restart=false;
stop=false;
remove=false;
rc=0

while [[ $# -gt 0 ]]
do
  key="$1"
  case $key in

    -help|-h)
      helpRequest=true
      print_help
      exit 0
      shift
      ;;
    -image-list)
      image_file_list="$2"
      echo "setting image_file_list to ${image_file_list}"
      shift
      ;;
    -env-props)
      env_properties="$2"
      echo "setting env_props to ${env_properties}"
      [ ! -f ${env_properties} ] && { echo env file "${env_properties}" not found; exit 1; }
      shift
      ;;
    -registry-namespace)
      registry_namespace="$2"
      echo "setting registry_namespace to ${registry_namespace}"
      shift
      ;;
    -registry)
      registry="$2"
      echo "setting registry to ${registry}"
      shift
      ;;
    -restart)
      echo "restarting acd configuration editor"
      restart=true;
      shift
      ;;
    -stop)
      echo "stopping acd configuration editor"
      stop=true;
      shift
      ;;
    -remove)
      echo "removing acd configuration editor"
      remove=true;
      shift
      ;;
    *)
      echo "Unknown paramater ${key}".
      print_help
      exit 1
  esac
  shift
done

# Parameters checking

#########################################################################
#Mainline
#########################################################################


# first stop any running containers
# The following has problems when no containers are running
# docker container ls | grep -v CONTAINER | awk '{print $1}' | xargs -L1 docker container stop
echo " stopping all running containers..."
docker container ls | grep -v CONTAINER | awk '{print $1}' | xargs -n 1 -I {} docker container stop {}
echo " ...containers stopped!"

# if stop option was used that is all we do
if [ ${stop} = true ]; then
   exit $rc;
fi

# if just restarting skip the image reload
if [ ${restart} != true ]; then
  echo "image_file_list : ${image_file_list}"
  # now remove all containers
  docker container ls --all | grep -v CONTAINER | awk '{print $1}' | xargs -n 1 -I {} docker container rm {}
  # remove all existing images first otherwise it may rename ones
  # now remove all images that are in some acd namespace
  docker images | grep -v REPOSITORY | grep acd | awk '{print $1}' | xargs -n 1 -I {} docker rmi {}
  [ ! -f $image_file_list ] && { echo image list file "$image_file_list" not found; exit 1; }

# if asked to remove we stop after removing the containers and images
  if [ ${remove} = true ]; then
    echo "ACD containers stopped and images removed. Attempting to remove network."
    docker network rm service_bridge
    exit $rc;
  fi
  # load up the images from the shipped files
  while read -r image_name
  do
    if  ! echo "${image_name}" | grep -q '^ *#'   # ignore comments
    then
      image_file="${image_name}.tar.gz"
      if [[ -f ${image_file} ]]
      then
        echo " loading  ${image_file}"
        load_image "${image_file}"
      else
        echo " skipping loading image from local file ${image_file}"
      fi
    fi
  done < "${image_file_list}"
fi
# start containers for acd, dictionary and cartridge service

# update acd_ce.properties w/ external host name

# Install cacerts to truststore - need to create empty trust store first ...
# keytool -importkeystore -srckeystore /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-1.el7_7.x86_64/jre/lib/security/cacerts -destkeystore /tmp/installs/config/truststore/trust.jks -srcstorepass changeit -deststorepass wats0n
# start up all containers for acd_ce
[ ! -f ${env_properties} ] && { echo "${env_properties}" not found; exit 1; }
./docker_deploy_service.sh -environment_properties ${env_properties} -image_list ${image_file_list} -registry_namespace ${registry_namespace} -registry ${registry} -store_password wats0n
echo "done"
exit $rc
./Docker/service_generate_effective_properties.sh000755 000766 000024 00000041266 14427433530 023221 0ustar00dweberstaff000000 000000 #!/bin/bash
# ***************************************************************** 
#                                                                   
# Merative Confidential                                             
#                                                                   
# (C) Copyright Merative US L.P. 2001, 2023 
#                                                                   
# ***************************************************************** 

BASE_DIR="$(cd "$(dirname "$0")"/../..; pwd -P)"
BASE_SCRIPT_DIR="$(cd "$(dirname "$0")"/..; pwd -P)"
SCRIPT_NAME="$(basename "$0")"
UNAME="$(uname -s)"
echo "####################"
echo "Executing $SCRIPT_NAME"

#########################################################################
#Common functions
#########################################################################

#########################################################################
#Parameter management
#########################################################################
#Parameter defaults
endpoint=s3.us-south.cloud-object-storage.appdomain.cloud
secret_dir=
service_name=
staging_dir=.

while [[ $# -gt 0 ]]
do
  key="$1"
  case $key in
    -component_name)
      component_name="$2"
      echo "component_name=${component_name}"
      shift
      ;;
    -cos_access_id_builds)
      cos_access_id_builds="$2"
      echo "cos_access_id_builds=${cos_access_id_builds}"
      shift
      ;;
    -cos_access_secret_builds)
      cos_access_secret_builds="$2"
      shift
      ;;
    -encryption_enabled)
      encryption_enabled="$2"
      shift
      ;;
    -endpoint)
      endpoint="$2"
      echo "endpoint=${endpoint}"
      shift
      ;;
    -env_group)
      env_group="$2"
      echo "env_group=${env_group}"
      shift
      ;;
    -env_props)
      env_props="$2"
      echo "env_props=${env_props}"
      shift
      ;;
    -secret_dir)
      secret_dir="$2"
      echo "secret_dir=${secret_dir}"
      shift
      ;;
    -service_name)
      service_name="$2"
      echo "service_name=${service_name}"
      shift
      ;;
    -stage)
      stage="$2"
      echo "stage=${stage}"
      stage_upper=$(echo "${stage}" | perl -ne 'print uc')
      shift
      ;;
    -staging_dir)
      staging_dir="$2"
      echo "staging_dir=${staging_dir}"
      shift
      ;;
    *)
      echo "Unknown parameter $1"
  esac
  shift
done

#Required parameters
if [ -z "${service_name}" ]; then
  service_name=$(echo "${component_name}" | perl -p -e 's/WHCS_//g' | perl -p -e 's/_Service//g' | perl -ne 'print lc' | sed "s#_#-#g")
fi
if [ -z "${env_props}" ]; then
  echo "Missing required parameter env_props"
  exit 1
fi
if [ -z "${stage}" ]; then
  echo "Missing required parameter stage"
  exit 1
fi
if [ "${stage}" != "install" ] && [ "${stage}" != "runtime" ]; then
  echo "Invalid parameter stage"
  exit 1
fi

#########################################################################
#Mainline
#########################################################################
set +o errexit

if [ ! -z "${secret_dir}" ]; then
  cos_access_id_builds_encrypted=$(cat ${secret_dir}/whcs_devops_cos/username)
  if [ $? != 0 ]; then
    echo "Retrieve local build id failed"
    exit 1
  fi
  if [ ! -z "${encryption_enabled}" ] && [ "${encryption_enabled}" == "true" ]; then
        cos_access_id_builds=$(java -cp ${BASE_DIR}/whcs-devops-ucd/tools/service-encryption.jar com.ibm.watson.health.services.Encryption -d ${cos_access_id_builds_encrypted})
    if [ $? != 0 ]; then
      echo "Decrypting local build id failed"
      exit 1
    fi
  else
        cos_access_id_builds=${cos_access_id_builds_encrypted}
  fi
  echo "cos_access_id_builds: ${cos_access_id_builds}"

  cos_access_secret_builds_encrypted=$(cat ${secret_dir}/whcs_devops_cos/password)
  if [ $? != 0 ]; then
    echo "Retrieve local build secret failed"
    exit 1
  fi
  if [ ! -z "${encryption_enabled}" ] && [ "${encryption_enabled}" == "true" ]; then
        cos_access_secret_builds=$(java -cp ${BASE_DIR}/whcs-devops-ucd/tools/service-encryption.jar com.ibm.watson.health.services.Encryption -d ${cos_access_secret_builds_encrypted})
    if [ $? != 0 ]; then
      echo "Decrypting local build secret failed"
      exit 1
    fi
  else
        cos_access_secret_builds=${cos_access_secret_builds_encrypted}
  fi
fi

# Retrieve environment properties, unless it's a micro service without properties (concept disambiguation stack)
if [ -e "${staging_dir}/${env_props}.properties" ]; then
  echo "Env props found in staging directory"
elif [ -e "${env_props}" ]; then
  echo "Retrieving env props from specified location"
  echo "rsync -r -L -verbose ${env_props} ${staging_dir}"
  rsync -r -L -verbose ${env_props} ${staging_dir}
  RC=$?
  if [ $RC != 0 ]; then
    echo "rsync failed with rc=$RC"
    exit 1
  fi
else
  echo "Retrieving env props from COS"
  if [ -e "${staging_dir}/${env_props}" ]; then
    echo "Env props already existed locally, skipping COS"
  else
    bucket="ibm.wh.whcs.environments"
    object_dir="env_groups/${env_group}"
    object="${env_props}.properties"
    ${BASE_SCRIPT_DIR}/cos/cos_get.sh -accessKey "${cos_access_id_builds}" \
        -accessSecret "${cos_access_secret_builds}" \
        -bucket "${bucket}" \
        -encryption_enabled "${encryption_enabled}" \
        -endpoint ${endpoint} \
        -object "${object_dir}/${object}" \
        -secret_dir "${secret_dir}"
    if [ $? != 0 ]; then
      echo "Primary artifact download failed."
      exit 1;
    fi
    mv -f ${bucket}/${object_dir}/${object} ${staging_dir}
    rm -rf ${bucket}
  fi
fi

# Generate ${stage} properties
object="${staging_dir}/${env_props}.properties"
# Source env props to get modifiers for later (Must be done prior to service props)
. ${object}
if [ $? != 0 ]; then
  echo "${object} not found"
  exit 1
fi

service_name_suffix=`echo ${service_name} | sed "s#-#_#g" | perl -ne 'print uc'`

override_prop_array_orig=$(perl -pe 's/\\\n//' ${object} | grep OVERRIDE_${stage_upper}_PROPERTIES_${service_name_suffix} | perl -pe "s/OVERRIDE_${stage_upper}_PROPERTIES_${service_name_suffix}=//" | tr ';' '\n')
echo "$override_prop_array_orig"
> ${staging_dir}/service_${stage}.properties
partial_value=""
for array_value in ${override_prop_array_orig[@]}; do
  if [[ "${array_value}" == *"=\""* ]] && [[ "${array_value}" != *"\"" ]]; then
    partial_value="${array_value}"
  elif [ -z "${partial_value}" ]; then
    echo "${array_value}" >> ${staging_dir}/service_${stage}.properties
  elif [[ "${array_value}" == *"\"" ]]; then
    echo "${partial_value}\;${array_value}" >> ${staging_dir}/service_${stage}.properties
    partial_value=""
  else
    partial_value+="\;${array_value}"
  fi
done
echo "==================================================="
echo "====== Start of service_${stage}.properties ========"
cat ${staging_dir}/service_${stage}.properties
echo "====== End of service_${stage}.properties =========="
echo "==================================================="

override_prop_array_orig=$(perl -pe 's/\\\n//' ${object} | grep ENV_OVERRIDE_${stage_upper}_PROPERTIES | perl -pe "s/ENV_OVERRIDE_${stage_upper}_PROPERTIES=//" | tr ';' '\n')
echo "$override_prop_array_orig"
> ${staging_dir}/environment_${stage}.properties
partial_value=""
for array_value in ${override_prop_array_orig[@]}; do
  if [[ "${array_value}" == *"=\""* ]] && [[ "${array_value}" != *"\"" ]]; then
    partial_value="${array_value}"
  elif [ -z "${partial_value}" ]; then
    echo "${array_value}" >> ${staging_dir}/environment_${stage}.properties
  elif [[ "${array_value}" == *"\"" ]]; then
    echo "${partial_value}\;${array_value}" >> ${staging_dir}/environment_${stage}.properties
    partial_value=""
  else
    partial_value+="\;${array_value}"
  fi
done
echo "==================================================="
echo "====== Start of environment_${stage}.properties ===="
cat ${staging_dir}/environment_${stage}.properties
echo "====== End of environment_${stage}.properties ======"
echo "==================================================="

awk -F= '!a[$1]++' ${staging_dir}/service_${stage}.properties ${staging_dir}/environment_${stage}.properties > ${staging_dir}/${stage}_effective.properties
#rm -f ${staging_dir}/service_${stage}.properties
#rm -f ${staging_dir}/environment_${stage}.properties

#Source ${stage} and environment properties
. ${staging_dir}/${stage}_effective.properties
if [ $? != 0 ]; then
  echo "${staging_dir}/${stage}_effective.properties not found"
  exit 1
fi

if [ "${stage}" == "runtime" ]; then
  context_root=$(echo "services/${service_name}" | sed "s#-#_#g")
  service_name_install=${service_name}
  if [ ! -z "$ENV_NAME_MODIFIER" ] ; then
    service_name=${service_name}-${ENV_NAME_MODIFIER}
    context_root=${context_root}_${ENV_NAME_MODIFIER}
  fi

  if [ ! -z "${com_ibm_watson_health_common_service_name_install}" ]; then
    echo "Setting com_ibm_watson_health_common_service_name_install to ${service_name_install} in ${stage}_effective.properties"
    echo "com_ibm_watson_health_common_service_name_install=${service_name_install}" >> ${staging_dir}/${stage}_effective.properties
    export clinical_data_annotator_common_service_name_install=${com_ibm_watson_health_common_service_name_install}
    echo "clinical_data_annotator_common_service_name_install=${service_name_install}" >> ${staging_dir}/${stage}_effective.properties
  fi
  if [ ! -z "${clinical_data_annotator_common_service_name_install}" ]; then
    echo "Setting clinical_data_annotator_common_service_name_install to ${service_name_install} in ${stage}_effective.properties"
    echo "clinical_data_annotator_common_service_name_install=${service_name_install}" >> ${staging_dir}/${stage}_effective.properties
    export com_ibm_watson_health_common_service_name_install=${clinical_data_annotator_common_service_name_install}
    echo "com_ibm_watson_health_common_service_name_install=${service_name_install}" >> ${staging_dir}/${stage}_effective.properties
  fi
  if [ ! -z "${com_ibm_watson_health_common_service_name}" ]; then
    echo "Setting com_ibm_watson_health_common_service_name to ${service_name} in ${stage}_effective.properties"
    echo "com_ibm_watson_health_common_service_name=${service_name}" >> ${staging_dir}/${stage}_effective.properties
    export clinical_data_annotator_common_service_name=${com_ibm_watson_health_common_service_name}
    echo "clinical_data_annotatorh_common_service_name=${service_name}" >> ${staging_dir}/${stage}_effective.properties
  fi
  if [ ! -z "${clinical_data_annotator_common_service_name}" ];then
    echo "Setting clinical_data_annotator_common_service_name to ${service_name} in ${stage}_effective.properties"
    echo "clinical_data_annotator_common_service_name=${service_name}" >> ${staging_dir}/${stage}_effective.properties
    export com_ibm_watson_health_common_service_name=${clinical_data_annotator_common_service_name}
    echo "com_ibm_watson_health_common_service_name=${service_name}" >> ${staging_dir}/${stage}_effective.properties
  fi
  if [ ! -z "${com_ibm_watson_health_common_context_root}" ]; then
    echo "Setting com_ibm_watson_health_common_context_root to ${context_root} in ${stage}_effective.properties"
    echo "com_ibm_watson_health_common_context_root=${context_root}" >> ${staging_dir}/${stage}_effective.properties
    export clinical_data_annotator_common_context_root=${com_ibm_watson_health_common_context_root}
    echo "clinical_data_annotator_common_context_root=${context_root}" >> ${staging_dir}/${stage}_effective.properties
  fi
  if [ ! -z "${clinical_data_annotator_common_context_root}" ]; then
    echo "Setting clinical_data_annotator_common_context_root to ${context_root} in ${stage}_effective.properties"
    echo "clinical_data_annotator_common_context_root=${context_root}" >> ${staging_dir}/${stage}_effective.properties
    export com_ibm_watson_health_common_context_root=${clinical_data_annotator_common_context_root}
    echo "com_ibm_watson_health_common_context_root=${context_root}" >> ${staging_dir}/${stage}_effective.properties
  fi

# Disable this temporarily
  # if [ -z "${com_ibm_watson_health_common_javax_net_debug}" ]; then
  #     echo "Setting com_ibm_watson_health_common_javax_net_debug to none"
  #     echo "com_ibm_watson_health_common_javax_net_debug=none" >> ${staging_dir}/${stage}_effective.properties
  # fi
  
  if [ ! -z "$ENV_PORT_MODIFIER" ] ; then
    if [ "$com_ibm_watson_health_common_http_port" != "-1" ]; then
      propertyValueHttp=$((com_ibm_watson_health_common_http_port + ENV_PORT_MODIFIER))
      echo "updating com_ibm_watson_health_common_http_port to ${propertyValueHttp} in ${stage}_effective.properties"
      export clinical_data_annotator_common_http_port=$com_ibm_watson_health_common_http_port
    fi
    if [ "$clinical_data_annotator_common_http_port" != "-1" ]; then
      propertyValueHttp=$((clinical_data_annotator_common_http_port + ENV_PORT_MODIFIER))
      echo "updating clinical_data_annotator_common_http_port to ${propertyValueHttp} in ${stage}_effective.properties"
      export com_ibm_watson_health_common_http_port=$clinical_data_annotator_common_http_port
    fi
    if [ "$com_ibm_watson_health_common_https_port" != "-1" ]; then
      propertyValueHttps=$((com_ibm_watson_health_common_https_port + ENV_PORT_MODIFIER))
      echo "updating com_ibm_watson_health_common_https_port to ${propertyValueHttps} in ${stage}_effective.properties"
      export clinical_data_annotator_common_https_port=$com_ibm_watson_health_common_https_port
    fi
    if [ "$clinical_data_annotator_common_https_port" != "-1" ]; then
      propertyValueHttps=$((clinical_data_annotator_common_https_port + ENV_PORT_MODIFIER))
      echo "updating clinical_data_annotator_common_https_port to ${propertyValueHttps} in ${stage}_effective.properties"
      export com_ibm_watson_health_common_https_port=$clinical_data_annotator_common_https_port
    fi
    if [[ $UNAME == Darwin* ]]; then
      if [ "$com_ibm_watson_health_common_http_port" != "-1" ]; then
        sed -i '' "s#\(com_ibm_watson_health_common_http_port=\).*\$#\1${propertyValueHttp}#" ${staging_dir}/${stage}_effective.properties
        echo "clinical_data_annotator_common_http_port=${propertyValueHttp}" >> ${staging_dir}/${stage}_effective.properties
      fi
      if [ "$clinical_data_annotator_common_http_port" != "-1" ]; then
        sed -i '' "s#\(clinical_data_annotator_common_http_port=\).*\$#\1${propertyValueHttp}#" ${staging_dir}/${stage}_effective.properties
        echo "com_ibm_watson_health_common_http_port=${propertyValueHttp}" >> ${staging_dir}/${stage}_effective.properties
      fi
      if [ "$com_ibm_watson_health_common_https_port" != -1 ]; then
        sed -i '' "s#\(com_ibm_watson_health_common_https_port=\).*\$#\1${propertyValueHttps}#" ${staging_dir}/${stage}_effective.properties
        echo "clinical_data_annotator_common_https_port=${propertyValueHttps}" >> ${staging_dir}/${stage}_effective.properties
      fi
      if [ "$clinical_data_annotator_common_https_port" != -1 ]; then
        sed -i '' "s#\(clinical_data_annotator_common_https_port=\).*\$#\1${propertyValueHttps}#" ${staging_dir}/${stage}_effective.properties
        echo "com_ibm_watson_health_common_https_port=${propertyValueHttps}" >> ${staging_dir}/${stage}_effective.properties
      fi
    else
      if [ "$com_ibm_watson_health_common_http_port" != "-1" ]; then
        sed -i'' "s#\(com_ibm_watson_health_common_http_port=\).*\$#\1${propertyValueHttp}#" ${staging_dir}/${stage}_effective.properties
        echo "clinical_data_annotator_common_http_port=${propertyValueHttp}" >> ${staging_dir}/${stage}_effective.properties
      fi
      if [ "$clinical_data_annotator_common_http_port" != "-1" ]; then
        sed -i'' "s#\(clinical_data_annotator_common_http_port=\).*\$#\1${propertyValueHttp}#" ${staging_dir}/${stage}_effective.properties
        echo "com_ibm_watson_health_common_http_port=${propertyValueHttp}" >> ${staging_dir}/${stage}_effective.properties
      fi
      if [ "$com_ibm_watson_health_common_https_port" != -1 ]; then
        sed -i'' "s#\(com_ibm_watson_health_common_https_port=\).*\$#\1${propertyValueHttps}#" ${staging_dir}/${stage}_effective.properties
        echo "clinical_data_annotator_common_https_port=${propertyValueHttps}" >> ${staging_dir}/${stage}_effective.properties
      fi
      if [ "$clinical_data_annotator_common_https_port" != -1 ]; then
        sed -i'' "s#\(clinical_data_annotator_common_https_port=\).*\$#\1${propertyValueHttps}#" ${staging_dir}/${stage}_effective.properties
        echo "com_ibm_watson_health_common_https_port=${propertyValueHttps}" >> ${staging_dir}/${stage}_effective.properties
      fi
    fi
  fi
fi

echo "==================================================="
echo "====== Start of ${stage}_effective.properties ======"
cat ${staging_dir}/${stage}_effective.properties
echo "====== End of ${stage}_effective.properties ========"
echo "==================================================="
./Docker/acd-ce.properties000755 000766 000024 00000023325 14427157215 016310 0ustar00dweberstaff000000 000000 ENV_DEPLOY_CONTROLLER=DOCKER
ENV_SYSTEMS=localhost
ENV_OVERRIDE_RUNTIME_PROPERTIES=\
clinical_data_annotator_common_docker_user="1001:0";\
clinical_data_annotator_common_docker_volume="%HOME%/acd-ce/installs/config:%HOME%/acd-ce/installs/config:z";\
clinical_data_annotator_common_enabled_dark_features=none;\
clinical_data_annotator_common_global_config_dir=%HOME%/acd-ce/installs/config;\
clinical_data_annotator_common_http_port=-1;\
clinical_data_annotator_common_shared_config_dir=%HOME%/acd-ce/installs/config;\
clinical_data_annotator_common_concurrent_blocking_threshold=5;\
clinical_data_annotator_common_concurrent_reject_threshold=16; \
clinical_data_annotator_common_client_auth_enabled=false

BUILD_NAME_ADVANCED_CARE_INSIGHTS=Advanced_Care_Insights_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_ADVANCED_CARE_INSIGHTS=\
clinical_data_annotator_common_service_name=advanced-care-insights;\
clinical_data_annotator_common_context_root=advanced_care_insights;\
clinical_data_annotator_common_https_port=9246;\
clinical_data_annotator_common_max_heap=4608M;\
clinical_data_annotator_common_min_heap=4608M;

BUILD_NAME_ATTRIBUTE_DETECTION=Attribute_Detection_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_ATTRIBUTE_DETECTION=\
clinical_data_annotator_common_service_name=attribute-detection;\
clinical_data_annotator_common_context_root=attribute_detection;\
clinical_data_annotator_common_https_port=9275;\
clinical_data_annotator_common_max_heap=1G;\
clinical_data_annotator_common_min_heap=1G;

BUILD_NAME_CARTRIDGE=Cartridge_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_CARTRIDGE=\
clinical_data_annotator_common_service_name=cartridge;\
clinical_data_annotator_common_context_root=cartridge;\
clinical_data_annotator_common_https_port=9281;\
clinical_data_annotator_common_max_heap=1G;\
clinical_data_annotator_common_min_heap=1G;\
clinical_data_annotator_car_acd_sandbox_url=https://%SERVER%/services/clinical_data_annotator;\
clinical_data_annotator_car_acd_target_url=https://%SERVER%/services/clinical_data_annotator;\
clinical_data_annotator_car_url=https://%SERVER%/services/cartridge;\
clinical_data_annotator_car_acd_sandbox_internal_url=https://clinical-data-annotator:9443/services/clinical_data_annotator;\
clinical_data_annotator_car_acd_target_internal_url=https://clinical-data-annotator:9443/services/clinical_data_annotator;\
clinical_data_annotator_car_aci_internal_url=https://advanced-care-insights:9443/services/advanced_care_insights;\
clinical_data_annotator_car_av_internal_url=https://attribute-detection:9443/services/attribute_detection;\
clinical_data_annotator_car_cd_internal_url=https://concept-detection:9443/services/concept_detection;\
clinical_data_annotator_car_cdc_internal_url=https://concept-dictionary:9443/services/concept_dictionary;\
clinical_data_annotator_car_cds_internal_url=https://concept-disambiguation:9443/services/concept_disambiguation;\
clinical_data_annotator_car_hyp_internal_url=https://hypothetical-detection:9443/services/hypothetical_detection;\
clinical_data_annotator_car_neg_internal_url=https://negation-detection:9443/services/negation_detection;\
clinical_data_annotator_car_ont_internal_url=https://ontology:9443/services/ontology;\
clinical_data_annotator_car_spl_internal_url=https://spell-checker:9443/services/spell_checker;\
clinical_data_annotator_car_auth_header_email=;\
clinical_data_annotator_car_auth_header_firstname=;\
clinical_data_annotator_car_auth_header_lastname=;\
clinical_data_annotator_car_auth_header_fullname=;\
clinical_data_annotator_car_api_request_timeout_read=120000;\
clinical_data_annotator_car_api_request_timeout_connection=5000;

BUILD_NAME_CLINICAL_DATA_ANNOTATOR=Clinical_Data_Annotator_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_CLINICAL_DATA_ANNOTATOR=\
clinical_data_annotator_common_service_name=clinical-data-annotator;\
clinical_data_annotator_common_context_root=clinical_data_annotator;\
clinical_data_annotator_common_https_port=9272;\
clinical_data_annotator_common_max_heap=2G;\
clinical_data_annotator_acd_micro_aci_enable=true;\
clinical_data_annotator_acd_micro_aci_url=https://advanced-care-insights:9443/services/advanced_care_insights;\
clinical_data_annotator_acd_micro_av_enable=true;\
clinical_data_annotator_acd_micro_av_url=https://attribute-detection:9443/services/attribute_detection;\
clinical_data_annotator_acd_micro_cd_enable=true;\
clinical_data_annotator_acd_micro_cd_url=https://concept-detection:9443/services/concept_detection;\
clinical_data_annotator_acd_micro_cd_dark_enable=true;\
clinical_data_annotator_acd_micro_cd_dark_url=https://concept-detection:9443/services/concept_detection;\
clinical_data_annotator_acd_micro_cds_enable=true;\
clinical_data_annotator_acd_micro_cds_url=https://concept-disambiguation:9443/services/concept_disambiguation;\
clinical_data_annotator_acd_micro_cv_enable=true;\
clinical_data_annotator_acd_micro_cv_url=https://concept-value-detection:9443/services/concept_value_detection;\
clinical_data_annotator_acd_micro_hyp_enable=true;\
clinical_data_annotator_acd_micro_hyp_url=https://hypothetical-detection:9443/services/hypothetical_detection;\
clinical_data_annotator_acd_micro_mod_enable=true;\
clinical_data_annotator_acd_micro_mod_url=https://model-broker:9443/services/model_broker;\
clinical_data_annotator_acd_micro_neg_enable=true;\
clinical_data_annotator_acd_micro_neg_url=https://negation-detection:9443/services/negation_detection;\
clinical_data_annotator_acd_micro_ont_enable=true;\
clinical_data_annotator_acd_micro_ont_url=https://ontology:9443/services/ontology;\
clinical_data_annotator_acd_micro_spl_enable=true;\
clinical_data_annotator_acd_micro_spl_url=https://spell-checker:9443/services/spell_checker;\
clinical_data_annotator_common_min_heap=2G;\
clinical_data_annotator_common_concurrent_uri_pattern_list=/v1/analyze.*;

BUILD_NAME_CONCEPT_DETECTION=Concept_Detection_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_CONCEPT_DETECTION=\
clinical_data_annotator_common_service_name=concept-detection;\
clinical_data_annotator_common_context_root=concept_detection;\
clinical_data_annotator_common_https_port=9206;\
clinical_data_annotator_common_max_heap=9G;\
clinical_data_annotator_common_min_heap=6G;\
clinical_data_annotator_cd_cdc_service_url=https://concept-dictionary:9443/services/concept_dictionary;

BUILD_NAME_CONCEPT_DICTIONARY=Concept_Dictionary_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_CONCEPT_DICTIONARY=\
clinical_data_annotator_common_service_name=concept-dictionary;\
clinical_data_annotator_common_context_root=concept_dictionary;\
clinical_data_annotator_common_https_port=9256;\
clinical_data_annotator_common_max_heap=16G;\
clinical_data_annotator_common_min_heap=8G;

BUILD_NAME_CONCEPT_DISAMBIGUATION=Concept_Disambiguation_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_CONCEPT_DISAMBIGUATION=\
clinical_data_annotator_common_service_name=concept-disambiguation;\
clinical_data_annotator_common_context_root=concept_disambiguation;\
clinical_data_annotator_common_docker_shared_memory_size="4.5g";\
clinical_data_annotator_common_https_port=9273;\
clinical_data_annotator_common_max_heap=512M;\
clinical_data_annotator_common_min_heap=512M;\
clinical_data_annotator_cds_server_processes=4;

BUILD_NAME_CONCEPT_VALUE_DETECTION=Concept_Value_Detection_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_CONCEPT_VALUE_DETECTION=\
clinical_data_annotator_common_service_name=concept-value-detection;\
clinical_data_annotator_common_context_root=concept_value_detection;\
clinical_data_annotator_common_https_port=9208;\
clinical_data_annotator_common_max_heap=1G;\
clinical_data_annotator_common_min_heap=1G;

BUILD_NAME_HYPOTHETICAL_DETECTION=Hypothetical_Detection_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_HYPOTHETICAL_DETECTION=\
clinical_data_annotator_common_service_name=hypothetical-detection;\
clinical_data_annotator_common_context_root=hypothetical_detection;\
clinical_data_annotator_common_https_port=9209;\
clinical_data_annotator_common_max_heap=2G;\
clinical_data_annotator_common_min_heap=2G;

BUILD_NAME_MODEL_BROKER=Model_Broker_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_MODEL_BROKER=\
clinical_data_annotator_common_service_name=model-broker;\
clinical_data_annotator_common_context_root=model_broker;\
clinical_data_annotator_common_https_port=9278;\
clinical_data_annotator_common_max_heap=1400M;\
clinical_data_annotator_common_min_heap=1400M;\
clinical_data_annotator_common_max_bytes=500M;\
clinical_data_annotator_common_max_physical_bytes=600M;\
clinical_data_annotator_common_delegate_process_max_heap=300M;\
clinical_data_annotator_common_delegate_process_jobs_between_recycle=20000;

BUILD_NAME_NEGATION_DETECTION=Negation_Detection_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_NEGATION_DETECTION=\
clinical_data_annotator_common_service_name=negation-detection;\
clinical_data_annotator_common_context_root=negation_detection;\
clinical_data_annotator_common_https_port=9212;\
clinical_data_annotator_common_max_heap=2G;\
clinical_data_annotator_common_min_heap=2G;

BUILD_NAME_ONTOLOGY=Ontology_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_ONTOLOGY=\
clinical_data_annotator_common_service_name=ontology;\
clinical_data_annotator_common_context_root=ontology;\
clinical_data_annotator_common_https_port=9282;\
clinical_data_annotator_common_max_heap=1536M;\
clinical_data_annotator_common_min_heap=1536M;

BUILD_NAME_SPELL_CHECKER=Spell_Checker_Service_Build
OVERRIDE_RUNTIME_PROPERTIES_SPELL_CHECKER=\
clinical_data_annotator_common_service_name=spell-checker;\
clinical_data_annotator_common_context_root=spell_checker;\
clinical_data_annotator_common_https_port=9277;\
clinical_data_annotator_common_max_heap=1512M;\
clinical_data_annotator_common_min_heap=1512M;\
clinical_data_annotator_common_max_bytes=500M;\
clinical_data_annotator_common_max_physical_bytes=600M;\
clinical_data_annotator_common_delegate_process_max_heap=300M;\
clinical_data_annotator_common_delegate_process_jobs_between_recycle=50000;