update dependency version, modify memory defaults, and introduce tran…

…sactionTimeout

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

charts/ibm-fhir-server/Chart.yaml

@@ -27,3 +27,15 @@ annotations:
       description: align endpoints config with fhir-server-config.json's fhirServer/resources section
     - kind: changed
       description: updated to version 10.12.2 of the embedded bitnami postgresql chart
+    - kind: changed
+      description: updated the version of the bitnami postgresql image to 13.4.0-debian-10-r53
+    - kind: changed
+      description: mount jvm.options to overrides instead of overwriting the default jvm.options
+    - kind: added
+      description: transactionTimeout helm value for setting FHIR_TRANSACTION_MANAGER_TIMEOUT
+    - kind: removed
+      description: the default value for minHeap; instead we will defer to the IBM FHIR Server default
+    - kind: removed
+      description: the default value for maxHeap; instead we will defer to the JVM default
+    - kind: changed
+      description: reduced the default memory request to 1Gi and the default memory limit to 4Gi

charts/ibm-fhir-server/README.md

@@ -38,6 +38,7 @@ This design gives the deployer of this helm chart a number of different options
 1. Use the `defaultFhirServerConfig` named template that is provided, but override values specified in the template to customize the configuration. Chart values are used to customize config properties in the following sections of the configuration:
     - core
     - resources
+    - security
     - notifications
     - audit
     - persistence
@@ -209,8 +210,8 @@ If the `objectStorage.objectStorageSecret` value is set, this helm chart will on
 | ingress.rules[0].paths[0] | string | `"/"` |  |
 | ingress.servicePort | string | `"https"` |  |
 | ingress.tls[0].secretName | string | `""` |  |
-| maxHeap | string | `"4096m"` |  |
-| minHeap | string | `"1024m"` |  |
+| maxHeap | string | `""` | The value passed to the JVM via -Xmx to set the max heap size. |
+| minHeap | string | `""` | The value passed to the JVM via -Xms to set the initial heap size |
 | nameOverride | string | `nil` | Optional override for chart name portion of the created kube resources |
 | notifications.kafka.bootstrapServers | string | `nil` |  |
 | notifications.kafka.enabled | bool | `false` |  |
@@ -252,9 +253,9 @@ If the `objectStorage.objectStorageSecret` value is set, this helm chart will on
 | postgresql.postgresqlExtendedConf | object | `{"maxPreparedTransactions":24}` | Extended Runtime Config Parameters (appended to main or default configuration) |
 | replicaCount | int | `2` | The number of replicas for the externally-facing FHIR server pods |
 | resources.limits.ephemeral-storage | string | `"1Gi"` |  |
-| resources.limits.memory | string | `"5Gi"` |  |
+| resources.limits.memory | string | `"4Gi"` |  |
 | resources.requests.ephemeral-storage | string | `"1Gi"` |  |
-| resources.requests.memory | string | `"2Gi"` |  |
+| resources.requests.memory | string | `"1Gi"` |  |
 | restrictEndpoints | bool | `false` | Set to true to restrict the API to a particular set of resource type endpoints |
 | schemaMigration.enabled | bool | `true` |  |
 | schemaMigration.image.pullPolicy | string | `"Always"` |  |
@@ -270,6 +271,7 @@ If the `objectStorage.objectStorageSecret` value is set, this helm chart will on
 | security.smartScopes | list | openid, profile, fhirUser, launch/patient, offline_access, and a set of patient/<resource>.read scopes for a number of resource types. | OAuth 2.0 scopes to advertise from the server |
 | serverRegistryResourceProviderEnabled | bool | `false` | Indicates whether the server registry resource provider should be used by the FHIR registry component to access definitional resources through the persistence layer |
 | traceSpec | string | `"*=info"` | The trace specification to use for selectively tracing components of the IBM FHIR Server. The log detail level specification is in the following format: `component1=level1:component2=level2` See https://openliberty.io/docs/latest/log-trace-configuration.html for more information. |
+| transactionTimeout | string | `"120s"` |  |
 
 ----------------------------------------------
 Autogenerated from chart metadata using [helm-docs v1.5.0](https://github.com/norwoodj/helm-docs/releases/v1.5.0)

charts/ibm-fhir-server/README.md.gotmpl

@@ -38,6 +38,7 @@ This design gives the deployer of this helm chart a number of different options
 1. Use the `defaultFhirServerConfig` named template that is provided, but override values specified in the template to customize the configuration. Chart values are used to customize config properties in the following sections of the configuration:
     - core
     - resources
+    - security
     - notifications
     - audit
     - persistence

charts/ibm-fhir-server/templates/configMap.yaml

@@ -12,11 +12,14 @@ data:
   fhir-server-config.json: >
     {{- include .Values.fhirServerConfigTemplate . }}
   jvm.options: |
+    {{- if .Values.minHeap }}
     # Initial heap size
     -Xms{{ .Values.minHeap }}
-
+    {{- end }}
+    {{- if .Values.maxHeap }}
     # Maximum heap size
     -Xmx{{ .Values.maxHeap }}
+    {{- end }}
 
     {{- with .Values.extraJvmOptions }}
     {{ tpl . $ | nindent 4 }}

charts/ibm-fhir-server/templates/deployment.yaml

@@ -83,7 +83,7 @@ spec:
               mountPath: /opt/ol/wlp/usr/servers/defaultServer/config/default/extension-search-parameters.json
               subPath: extension-search-parameters.json
             - name: fhir-server-config
-              mountPath: /opt/ol/wlp/usr/servers/defaultServer/jvm.options
+              mountPath: /opt/ol/wlp/usr/servers/defaultServer/configDropins/overrides/jvm.options
               subPath: jvm.options
           {{- if .Values.exposeHttpEndpoint }}
             - name: fhir-server-config
@@ -115,6 +115,8 @@ spec:
             - name: FHIR_HOSTNAME
               value: "{{ tpl .Values.ingress.hostname $ }}"
             {{- end }}
+            - name: FHIR_TRANSACTION_MANAGER_TIMEOUT
+              value: "{{ .Values.transactionTimeout }}"
             - name: FHIR_DB_HOSTNAME
               value: "{{ include "fhir.database.host" $ }}"
             - name: FHIR_DB_PORT

charts/ibm-fhir-server/values.yaml

@@ -265,14 +265,17 @@ ingress:
     - secretName: ""
 resources:
   requests:
-    memory: "2Gi"
+    memory: "1Gi"
     ephemeral-storage: "1Gi"
   limits:
-    memory: "5Gi"
+    memory: "4Gi"
     ephemeral-storage: "1Gi"
 
-minHeap: "1024m"
-maxHeap: "4096m"
+transactionTimeout: "120s"
+# -- The value passed to the JVM via -Xms to set the initial heap size
+minHeap: ""
+# -- The value passed to the JVM via -Xmx to set the max heap size.
+maxHeap: ""
 extraJvmOptions: ""
 extraEnv: ""