Personal-Twin/hapi-fhir-jpaserver-starter
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' into cr-6.9.6-snapshot

Browse Source
This commit is contained in:
Justin McKelvy
2023-11-22 09:44:51 -07:00
committed by GitHub
parent 0cf1ec8a7e 21d51be451
commit aaa8a1f8cc
13 changed files with 223 additions and 165 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
.github/workflows/chart-test.yaml vendored
View File

@@ -15,7 +15,7 @@ jobs:
- name: Install helm-docs
working-directory: /tmp
env:
HELM_DOCS_URL: https://github.com/norwoodj/helm-docs/releases/download/v1.11.0/helm-docs_1.11.0_Linux_x86_64.tar.gz
HELM_DOCS_URL: https://github.com/norwoodj/helm-docs/releases/download/v1.11.3/helm-docs_1.11.3_Linux_x86_64.tar.gz
run: |
curl -LSs $HELM_DOCS_URL | tar xz && \
mv ./helm-docs /usr/local/bin/helm-docs && \
@@ -30,6 +30,7 @@ jobs:
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
with:
fetch-depth: 0
- name: Check if documentation is up-to-date
run: helm-docs && git diff --exit-code HEAD

6
Dockerfile
View File

@@ -1,7 +1,7 @@
FROM docker.io/library/maven:3.9.2-eclipse-temurin-17 AS build-hapi
FROM docker.io/library/maven:3.9.4-eclipse-temurin-17 AS build-hapi
WORKDIR /tmp/hapi-fhir-jpaserver-starter
ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.26.0
ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.31.0
RUN curl -LSsO https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases/download/v${OPENTELEMETRY_JAVA_AGENT_VERSION}/opentelemetry-javaagent.jar
COPY pom.xml .
@@ -12,7 +12,7 @@ COPY src/ /tmp/hapi-fhir-jpaserver-starter/src/
RUN mvn clean install -DskipTests -Djdk.lang.Process.launchMechanism=vfork
FROM build-hapi AS build-distroless
RUN mvn package spring-boot:repackage -Pboot
RUN mvn package -DskipTests spring-boot:repackage -Pboot
RUN mkdir /app && cp /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war

16
charts/hapi-fhir-jpaserver/Chart.yaml
View File

@@ -10,18 +10,18 @@ dependencies:
version: 12.5.6
repository: oci://registry-1.docker.io/bitnamicharts
condition: postgresql.enabled
appVersion: 6.6.0
version: 0.13.0
appVersion: 6.8.3
version: 0.14.0
annotations:
artifacthub.io/license: Apache-2.0
artifacthub.io/changes: |
# When using the list of objects option the valid supported kinds are
# added, changed, deprecated, removed, fixed, and security.
- kind: added
description: allow specifying application properties via yaml config
description: updated starter image to 6.8.3
- kind: fixed
description: incorrect handling of existing secret database config
- kind: added
description: allow setting resource limits and requests for the Helm test pods
- kind: changed
description: updated curl used by helm tests to version to v8.2.0
- kind: changed
description: allow disabling the liveness-, readiness-, and startup-probes entirely
description: support for using a non-admin user for the postgres database
- kind: added
description: ability to create a dedicated ServiceAccount

10
charts/hapi-fhir-jpaserver/README.md
View File

@@ -1,6 +1,6 @@
# HAPI FHIR JPA Server Starter Helm Chart
![Version: 0.13.0](https://img.shields.io/badge/Version-0.13.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 6.6.0](https://img.shields.io/badge/AppVersion-6.6.0-informational?style=flat-square)
![Version: 0.14.0](https://img.shields.io/badge/Version-0.14.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 6.8.3](https://img.shields.io/badge/AppVersion-6.8.3-informational?style=flat-square)
This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
@@ -36,7 +36,7 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| image.pullPolicy | string | `"IfNotPresent"` | image pullPolicy to use |
| image.registry | string | `"docker.io"` | registry where the HAPI FHIR server image is hosted |
| image.repository | string | `"hapiproject/hapi"` | the path inside the repository |
| image.tag | string | `"v6.6.0@sha256:c00367865ae5dad4e171cbb68bfc1c39818854079d1565bee4c86a45e78335d0"` | the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image. |
| image.tag | string | `"v6.8.3@sha256:6195f1116ebabfb0a608addde043b3e524c456c4d4f35b3d25025afd7dcd2e27"` | the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image. |
| imagePullSecrets | list | `[]` | image pull secrets to use when pulling the image |
| ingress.annotations | object | `{}` | provide any additional annotations which may be required. Evaluated as a template. |
| ingress.enabled | bool | `false` | whether to create an Ingress to expose the FHIR server HTTP endpoint |
@@ -73,6 +73,10 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| securityContext.seccompProfile.type | string | `"RuntimeDefault"` | |
| service.port | int | `8080` | port where the server will be exposed at |
| service.type | string | `"ClusterIP"` | service type |
| serviceAccount.annotations | object | `{}` | Annotations to add to the service account |
| serviceAccount.automount | bool | `true` | Automatically mount a ServiceAccount's API credentials? |
| serviceAccount.create | bool | `false` | Specifies whether a service account should be created. |
| serviceAccount.name | string | `""` | The name of the service account to use. If not set and create is true, a name is generated using the fullname template |
| tests.resources | object | `{}` | configure the test pods resource requests and limits |
| tolerations | list | `[]` | pod tolerations |
| topologySpreadConstraints | list | `[]` | pod topology spread configuration see: https://kubernetes.io/docs/concepts/workloads/pods/pod-topology-spread-constraints/#api |
@@ -139,4 +143,4 @@ kubectl port-forward -n observability service/simplest-query 16686:16686
and opening <http://localhost:16686/> in your browser.
----------------------------------------------
Autogenerated from chart metadata using [helm-docs v1.11.0](https://github.com/norwoodj/helm-docs/releases/v1.11.0)
Autogenerated from chart metadata using [helm-docs v1.11.3](https://github.com/norwoodj/helm-docs/releases/v1.11.3)

7
charts/hapi-fhir-jpaserver/ci/custom-postgres-user-values.yaml Normal file
View File

@@ -0,0 +1,7 @@
postgresql:
enabled: true
auth:
username: hapi_fhir_jpaserver_starter_user
database: hapi_fhir_jpaserver_starter
password: secret_user_password
postgresPassword: secret_postgres_password

41
charts/hapi-fhir-jpaserver/templates/_helpers.tpl
View File

@@ -50,6 +50,17 @@ app.kubernetes.io/name: {{ include "hapi-fhir-jpaserver.name" . }}
app.kubernetes.io/instance: {{ .Release.Name }}
{{- end }}
{{/*
Create the name of the service account to use
*/}}
{{- define "hapi-fhir-jpaserver.serviceAccountName" -}}
{{- if .Values.serviceAccount.create }}
{{- default (include "hapi-fhir-jpaserver.fullname" .) .Values.serviceAccount.name }}
{{- else }}
{{- default "default" .Values.serviceAccount.name }}
{{- end }}
{{- end }}
{{/*
Create a default fully qualified postgresql name.
We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
@@ -63,10 +74,12 @@ We truncate at 63 chars because some Kubernetes name fields are limited to this
Get the Postgresql credentials secret name.
*/}}
{{- define "hapi-fhir-jpaserver.postgresql.secretName" -}}
{{- if and (.Values.postgresql.enabled) (not .Values.postgresql.auth.existingSecret) -}}
{{- printf "%s" (include "hapi-fhir-jpaserver.postgresql.fullname" .) -}}
{{- else if and (.Values.postgresql.enabled) (.Values.postgresql.auth.existingSecret) -}}
{{- printf "%s" .Values.postgresql.auth.existingSecret -}}
{{- if .Values.postgresql.enabled -}}
{{- if .Values.postgresql.auth.existingSecret -}}
{{- printf "%s" .Values.postgresql.auth.existingSecret -}}
{{- else -}}
{{- printf "%s" (include "hapi-fhir-jpaserver.postgresql.fullname" .) -}}
{{- end -}}
{{- else }}
{{- if .Values.externalDatabase.existingSecret -}}
{{- printf "%s" .Values.externalDatabase.existingSecret -}}
@@ -80,10 +93,18 @@ Get the Postgresql credentials secret name.
Get the Postgresql credentials secret key.
*/}}
{{- define "hapi-fhir-jpaserver.postgresql.secretKey" -}}
{{- if (.Values.externalDatabase.existingSecret) -}}
{{- printf "%s" .Values.externalDatabase.existingSecretKey -}}
{{- if .Values.postgresql.enabled -}}
{{- if .Values.postgresql.auth.username -}}
{{- printf "%s" .Values.postgresql.auth.secretKeys.userPasswordKey -}}
{{- else -}}
{{- printf "%s" .Values.postgresql.auth.secretKeys.adminPasswordKey -}}
{{- end -}}
{{- else }}
{{- printf "postgres-password" -}}
{{- if .Values.externalDatabase.existingSecret -}}
{{- printf "%s" .Values.externalDatabase.existingSecretKey -}}
{{- else -}}
{{- printf "postgres-password" -}}
{{- end -}}
{{- end -}}
{{- end -}}
@@ -98,7 +119,11 @@ Add environment variables to configure database values
Add environment variables to configure database values
*/}}
{{- define "hapi-fhir-jpaserver.database.user" -}}
{{- ternary "postgres" .Values.externalDatabase.user .Values.postgresql.enabled -}}
{{- if .Values.postgresql.enabled -}}
{{- printf "%s" .Values.postgresql.auth.username | default "postgres" -}}
{{- else -}}
{{- printf "%s" .Values.externalDatabase.user -}}
{{- end -}}
{{- end -}}
{{/*

1
charts/hapi-fhir-jpaserver/templates/deployment.yaml
View File

@@ -26,6 +26,7 @@ spec:
imagePullSecrets:
{{- toYaml . | nindent 8 }}
{{- end }}
serviceAccountName: {{ include "hapi-fhir-jpaserver.serviceAccountName" . }}
securityContext:
{{- toYaml .Values.podSecurityContext | nindent 8 }}
initContainers:

13
charts/hapi-fhir-jpaserver/templates/serviceaccount.yaml Normal file
View File

@@ -0,0 +1,13 @@
{{- if .Values.serviceAccount.create -}}
apiVersion: v1
kind: ServiceAccount
metadata:
name: {{ include "hapi-fhir-jpaserver.serviceAccountName" . }}
labels:
{{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
{{- with .Values.serviceAccount.annotations }}
annotations:
{{- toYaml . | nindent 4 }}
{{- end }}
automountServiceAccountToken: {{ .Values.serviceAccount.automount }}
{{- end }}

18
charts/hapi-fhir-jpaserver/values.yaml
View File

@@ -7,7 +7,7 @@ image:
# -- the path inside the repository
repository: hapiproject/hapi
# -- the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image.
tag: "v6.6.0@sha256:c00367865ae5dad4e171cbb68bfc1c39818854079d1565bee4c86a45e78335d0"
tag: "v6.8.3@sha256:6195f1116ebabfb0a608addde043b3e524c456c4d4f35b3d25025afd7dcd2e27"
# -- image pullPolicy to use
pullPolicy: IfNotPresent
@@ -198,6 +198,17 @@ podDisruptionBudget:
# -- maximum unavailable instances
maxUnavailable: ""
serviceAccount:
# -- Specifies whether a service account should be created.
create: false
# -- Annotations to add to the service account
annotations: {}
# -- The name of the service account to use.
# If not set and create is true, a name is generated using the fullname template
name: ""
# -- Automatically mount a ServiceAccount's API credentials?
automount: true
metrics:
serviceMonitor:
# -- if enabled, creates a ServiceMonitor instance for Prometheus Operator-based monitoring
@@ -229,7 +240,7 @@ curl:
image:
registry: docker.io
repository: curlimages/curl
tag: 8.2.0@sha256:daf3f46a2639c1613b25e85c9ee4193af8a1d538f92483d67f9a3d7f21721827
tag: 8.4.0@sha256:4a3396ae573c44932d06ba33f8696db4429c419da87cbdc82965ee96a37dd0af
tests:
# -- configure the test pods resource requests and limits
@@ -242,7 +253,8 @@ tests:
# memory: 128Mi
# -- additional Spring Boot application config. Mounted as a file and automatically loaded by the application.
extraConfig: ""
extraConfig:
""
# # For example:
# |
# hapi:

51
pom.xml
View File

@@ -14,7 +14,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.10.0</version>
<version>6.10.0</version>
</parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -42,6 +42,15 @@
</repository>
</repositories>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>2.3.8</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
@@ -62,17 +71,7 @@
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
</dependency>
<dependency>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>2.3.3</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-ri</artifactId>
<version>2.3.5</version>
<type>pom</type>
</dependency>
<!-- Needed for Email subscriptions -->
<dependency>
<groupId>org.simplejavamail</groupId>
@@ -222,11 +221,6 @@
</dependency>
<!-- webjars -->
<dependency>
<groupId>org.webjars</groupId>
<artifactId>bootstrap</artifactId>
<version>5.1.3</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>Eonasdan-bootstrap-datetimepicker</artifactId>
@@ -262,6 +256,12 @@
<artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
@@ -329,7 +329,7 @@
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<version>4.1.0</version>
<version>4.2.0</version>
<scope>test</scope>
</dependency>
@@ -349,14 +349,14 @@
<dependency>
<groupId>io.micrometer</groupId>
<artifactId>micrometer-core</artifactId>
<version>1.9.4</version>
<version>1.11.3</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus -->
<dependency>
<groupId>io.micrometer</groupId>
<artifactId>micrometer-registry-prometheus</artifactId>
<version>1.9.4</version>
<version>1.11.3</version>
</dependency>
<dependency>
@@ -412,7 +412,12 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.2.0</version>
<version>3.6.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.1.2</version>
</plugin>
</plugins>
</pluginManagement>
@@ -440,7 +445,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<version>3.11.0</version>
<configuration>
<release>11</release>
</configuration>
@@ -591,7 +596,7 @@
-->
<!-- example of how to start the server using spring boot-->
<!-- mvn clean package spring-boot:repackage -Pboot && java -jar target/hapi-fhir-jpaserver.war -->
<!-- mvn clean package spring-boot:repackage -Pboot && java -jar target/ROOT.war -->
<!-- Use the boot profile for development and debugging options when using your IDE -->
<profile>

11
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
View File

@@ -6,9 +6,6 @@ import ca.uhn.fhir.jpa.api.config.JpaStorageSettings.ClientIdStrategyEnum;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
import ca.uhn.fhir.rest.api.EncodingEnum;
import org.cqframework.cql.cql2elm.CqlCompilerException;
import org.cqframework.cql.cql2elm.CqlTranslator;
import org.cqframework.cql.cql2elm.LibraryBuilder;
import org.hl7.fhir.r4.model.Bundle;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.boot.context.properties.EnableConfigurationProperties;
@@ -68,7 +65,6 @@ public class AppProperties {
private List<String> supported_resource_types = new ArrayList<>();
private List<Bundle.BundleType> allowed_bundle_types = null;
private Boolean narrative_enabled = true;
private Validation validation = new Validation();
private Map<String, Tester> tester = null;
private Logger logger = new Logger();
@@ -78,22 +74,17 @@ public class AppProperties {
private Boolean install_transitive_ig_dependencies = true;
private Boolean reload_existing_implementationguides = false;
private Map<String, PackageInstallationSpec> implementationGuides = null;
private Boolean cr_enabled = false;
private String staticLocation = null;
private String staticLocationPrefix = "/static";
private Boolean lastn_enabled = false;
private boolean store_resource_in_lucene_index_enabled = false;
private NormalizedQuantitySearchLevel normalized_quantity_search_level = NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED;
private Boolean use_apache_address_strategy = false;
private Boolean use_apache_address_strategy_https = false;
private Integer bundle_batch_pool_size = 20;
private Integer bundle_batch_pool_max_size = 100;
private final Set<String> local_base_urls = new HashSet<>();
private final List<String> custom_interceptor_classes = new ArrayList<>();
public String getStaticLocationPrefix() {

204
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java
View File

@@ -11,7 +11,6 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.jpa.starter.util.JpaHibernatePropertiesProvider;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
import ca.uhn.fhir.rest.server.mail.IMailSvc;
import ca.uhn.fhir.rest.server.mail.MailConfig;
import ca.uhn.fhir.rest.server.mail.MailSvc;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
@@ -139,111 +138,112 @@ public class FhirServerConfigCommon {
jpaStorageSettings.setLastNEnabled(true);
}
if (appProperties.getInline_resource_storage_below_size() != 0) {
jpaStorageSettings.setInlineResourceTextBelowSize(appProperties.getInline_resource_storage_below_size());
}
if(appProperties.getInline_resource_storage_below_size() != 0){
jpaStorageSettings.setInlineResourceTextBelowSize(appProperties.getInline_resource_storage_below_size());
}
jpaStorageSettings.setStoreResourceInHSearchIndex(appProperties.getStore_resource_in_lucene_index_enabled());
jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
jpaStorageSettings.setStoreResourceInHSearchIndex(appProperties.getStore_resource_in_lucene_index_enabled());
jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
if (appProperties.getAllowed_bundle_types() != null) {
jpaStorageSettings.setBundleTypesAllowedForStorage(
appProperties.getAllowed_bundle_types().stream().map(BundleType::toCode).collect(Collectors.toSet()));
}
jpaStorageSettings
.setDeferIndexingForCodesystemsOfSize(appProperties.getDefer_indexing_for_codesystems_of_size());
if (appProperties.getClient_id_strategy() == JpaStorageSettings.ClientIdStrategyEnum.ANY) {
jpaStorageSettings.setResourceServerIdStrategy(JpaStorageSettings.IdStrategyEnum.UUID);
jpaStorageSettings.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
}
// Parallel Batch GET execution settings
jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_size());
jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_max_size());
if (appProperties.getAllowed_bundle_types() != null) {
jpaStorageSettings.setBundleTypesAllowedForStorage(appProperties.getAllowed_bundle_types().stream().map(BundleType::toCode).collect(Collectors.toSet()));
}
storageSettings(appProperties, jpaStorageSettings);
return jpaStorageSettings;
jpaStorageSettings.setDeferIndexingForCodesystemsOfSize(appProperties.getDefer_indexing_for_codesystems_of_size());
if (appProperties.getClient_id_strategy() == JpaStorageSettings.ClientIdStrategyEnum.ANY) {
jpaStorageSettings.setResourceServerIdStrategy(JpaStorageSettings.IdStrategyEnum.UUID);
jpaStorageSettings.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
}
//Parallel Batch GET execution settings
jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_size());
jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_max_size());
storageSettings(appProperties, jpaStorageSettings);
return jpaStorageSettings;
}
@Bean
public YamlPropertySourceLoader yamlPropertySourceLoader() {
return new YamlPropertySourceLoader();
}
@Bean
public PartitionSettings partitionSettings(AppProperties appProperties) {
PartitionSettings retVal = new PartitionSettings();
// Partitioning
if (appProperties.getPartitioning() != null) {
retVal.setPartitioningEnabled(true);
retVal.setIncludePartitionInSearchHashes(appProperties.getPartitioning().getPartitioning_include_in_search_hashes());
if(appProperties.getPartitioning().getAllow_references_across_partitions()) {
retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.ALLOWED_UNQUALIFIED);
} else {
retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED);
}
}
return retVal;
}
@Primary
@Bean
public HibernatePropertiesProvider jpaStarterDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
return new JpaHibernatePropertiesProvider(myEntityManagerFactory);
}
protected StorageSettings storageSettings(AppProperties appProperties, JpaStorageSettings jpaStorageSettings) {
jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
jpaStorageSettings.setDefaultSearchParamsCanBeOverridden(appProperties.getAllow_override_default_search_params());
if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
jpaStorageSettings.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
jpaStorageSettings.setIndexIdentifierOfType(appProperties.getEnable_index_of_type());
return jpaStorageSettings;
}
@Lazy
@Bean
public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) {
DatabaseBlobBinaryStorageSvcImpl binaryStorageSvc = new DatabaseBlobBinaryStorageSvcImpl();
if (appProperties.getMax_binary_size() != null) {
binaryStorageSvc.setMaximumBinarySize(appProperties.getMax_binary_size());
}
return binaryStorageSvc;
}
@Bean
public IEmailSender emailSender(AppProperties appProperties) {
if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
return buildEmailSender(appProperties.getSubscription().getEmail());
}
// Return a dummy anonymous function instead of null. Spring does not like null beans.
// TODO Get the signature of ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory
// changed so it does not require an instance of an IEmailSender
return theDetails -> {};
}
private static IEmailSender buildEmailSender(AppProperties.Subscription.Email email) {
return new EmailSenderImpl(new MailSvc(new MailConfig()
.setSmtpHostname(email.getHost())
.setSmtpPort(email.getPort())
.setSmtpUsername(email.getUsername())
.setSmtpPassword(email.getPassword())
.setSmtpUseStartTLS(email.getStartTlsEnable())));
}
@Bean
public YamlPropertySourceLoader yamlPropertySourceLoader() {
return new YamlPropertySourceLoader();
}
@Bean
public PartitionSettings partitionSettings(AppProperties appProperties) {
PartitionSettings retVal = new PartitionSettings();
// Partitioning
if (appProperties.getPartitioning() != null) {
retVal.setPartitioningEnabled(true);
retVal.setIncludePartitionInSearchHashes(
appProperties.getPartitioning().getPartitioning_include_in_search_hashes());
if (appProperties.getPartitioning().getAllow_references_across_partitions()) {
retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.ALLOWED_UNQUALIFIED);
} else {
retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED);
}
}
return retVal;
}
@Primary
@Bean
public HibernatePropertiesProvider jpaStarterDialectProvider(
LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
return new JpaHibernatePropertiesProvider(myEntityManagerFactory);
}
protected StorageSettings storageSettings(AppProperties appProperties, JpaStorageSettings jpaStorageSettings) {
jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
jpaStorageSettings.setDefaultSearchParamsCanBeOverridden(appProperties.getAllow_override_default_search_params());
if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
jpaStorageSettings.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
jpaStorageSettings.setIndexIdentifierOfType(appProperties.getEnable_index_of_type());
return jpaStorageSettings;
}
@Lazy
@Bean
public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) {
DatabaseBlobBinaryStorageSvcImpl binaryStorageSvc = new DatabaseBlobBinaryStorageSvcImpl();
if (appProperties.getMax_binary_size() != null) {
binaryStorageSvc.setMaximumBinarySize(appProperties.getMax_binary_size());
}
return binaryStorageSvc;
}
@Bean
public IEmailSender emailSender(AppProperties appProperties) {
if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
MailConfig mailConfig = new MailConfig();
AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
mailConfig.setSmtpHostname(email.getHost());
mailConfig.setSmtpPort(email.getPort());
mailConfig.setSmtpUsername(email.getUsername());
mailConfig.setSmtpPassword(email.getPassword());
mailConfig.setSmtpUseStartTLS(email.getStartTlsEnable());
IMailSvc mailSvc = new MailSvc(mailConfig);
IEmailSender emailSender = new EmailSenderImpl(mailSvc);
return emailSender;
}
return null;
}
}

5
src/main/resources/application.yaml
View File

@@ -81,14 +81,13 @@ hapi:
# server_address: http://hapi.fhir.org/baseR4
# defer_indexing_for_codesystems_of_size: 101
# install_transitive_ig_dependencies: true
### tells the server whether to attempt to load IG resources that are already present
# reload_existing_implementationGuides : false
#implementationguides:
### example from registry (packages.fhir.org)
# swiss:
# name: swiss.mednet.fhir
# version: 0.8.0
# reloadExisting : false
# reloadExisting: false
# installMode: STORE_AND_INSTALL
# example not from registry
# ips_1_0_0:
# packageUrl: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz