Personal-Twin/hapi-fhir-jpaserver-starter
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Merge branch 'master' into rel_5_4_0

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# Conflicts:
#	src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java
This commit is contained in:
Frank Tao
2021-03-18 18:02:58 -04:00
parent da326875dd 390dad7974
commit d4a8995d8b
4 changed files with 244 additions and 141 deletions
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81
.github/workflows/build-images.yaml vendored Normal file
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@@ -0,0 +1,81 @@
name: Build Container Images
on:
push:
tags:
- "image/v*"
pull_request:
branches: [master]
jobs:
build:
name: Build
runs-on: ubuntu-20.04
steps:
- name: Docker meta
id: docker_meta
uses: crazy-max/ghaction-docker-meta@v1
with:
images: |
ghcr.io/hapifhir/hapi
docker.io/hapiproject/hapi
tag-sha: false
tag-match: "v(.*)"
# waiting for https://github.com/crazy-max/ghaction-docker-meta/issues/13 for a cleaner solution
- name: Docker distroless meta
id: docker_distroless_meta
uses: crazy-max/ghaction-docker-meta@v1
with:
images: |
ghcr.io/hapifhir/hapi
docker.io/hapiproject/hapi
tag-sha: false
tag-match: "v(.*)"
sep-tags: -distroless,
- name: Set up QEMU
uses: docker/setup-qemu-action@v1
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v1
- name: Login to DockerHub
uses: docker/login-action@v1
if: github.event_name != 'pull_request'
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Login to GitHub Container Registry
uses: docker/login-action@v1
if: github.event_name != 'pull_request'
with:
registry: ghcr.io
username: ${{ github.repository_owner }}
password: ${{ secrets.GHCR_TOKEN }}
- name: Cache Docker layers
uses: actions/cache@v2
with:
path: /tmp/.buildx-cache
key: ${{ runner.os }}-buildx-${{ github.sha }}
restore-keys: |
${{ runner.os }}-buildx-
- name: Build and push
id: docker_build
uses: docker/build-push-action@v2
with:
cache-from: type=local,src=/tmp/.buildx-cache
cache-to: type=local,dest=/tmp/.buildx-cache
push: ${{ github.event_name != 'pull_request' }}
tags: ${{ steps.docker_meta.outputs.tags }}
labels: ${{ steps.docker_meta.outputs.labels }}
- name: Build and push distroless
id: docker_build_distroless
uses: docker/build-push-action@v2
with:
cache-from: type=local,src=/tmp/.buildx-cache
cache-to: type=local,dest=/tmp/.buildx-cache
push: ${{ github.event_name != 'pull_request' }}
tags: ${{ steps.docker_distroless_meta.outputs.tags }}-distroless
labels: ${{ steps.docker_distroless_meta.outputs.labels }}
target: release-distroless
- name: Print image digests
run: |
echo ${{ steps.docker_build.outputs.digest }}
echo ${{ steps.docker_build_distroless.outputs.digest }}

15
Dockerfile
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@@ -7,6 +7,21 @@ RUN mvn -ntp dependency:go-offline
COPY src/ /tmp/hapi-fhir-jpaserver-starter/src/ COPY src/ /tmp/hapi-fhir-jpaserver-starter/src/
RUN mvn clean install -DskipTests RUN mvn clean install -DskipTests
FROM build-hapi AS build-distroless
RUN mvn package spring-boot:repackage -Pboot
RUN mkdir /app && \
cp /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war
FROM gcr.io/distroless/java-debian10:11 AS release-distroless
COPY --chown=nonroot:nonroot --from=build-distroless /app /app
EXPOSE 8080
# 65532 is the nonroot user's uid
# used here instead of the name to allow Kubernetes to easily detect that the container
# is running as a non-root (uid != 0) user.
USER 65532:65532
WORKDIR /app
CMD ["/app/main.war"]
FROM tomcat:9.0.38-jdk11-openjdk-slim-buster FROM tomcat:9.0.38-jdk11-openjdk-slim-buster
RUN mkdir -p /data/hapi/lucenefiles && chmod 775 /data/hapi/lucenefiles RUN mkdir -p /data/hapi/lucenefiles && chmod 775 /data/hapi/lucenefiles

25
README.md
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@@ -344,23 +344,14 @@ elasticsearch.schema_management_strategy=CREATE
Set `hapi.fhir.lastn_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable the $lastn operation on this server. Note that the $lastn operation relies on Elasticsearch, so for $lastn to work, indexing must be enabled using Elasticsearch. Set `hapi.fhir.lastn_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable the $lastn operation on this server. Note that the $lastn operation relies on Elasticsearch, so for $lastn to work, indexing must be enabled using Elasticsearch.
## Example of a Dockerfile based on distroless images (for lower footprint and improved security) ## Build the distroless variant of the image (for lower footprint and improved security)
```code The default Dockerfile contains a `release-distroless` stage to build a variant of the image
FROM maven:3.6.3-jdk-11-slim as build-hapi using the `gcr.io/distroless/java-debian10:11` base image:
WORKDIR /tmp/hapi-fhir-jpaserver-starter
COPY pom.xml . ```sh
RUN mvn -ntp dependency:go-offline docker build --target=release-distroless -t hapi-fhir:distroless .
COPY src/ /tmp/hapi-fhir-jpaserver-starter/src/
RUN mvn clean package spring-boot:repackage -Pboot
FROM gcr.io/distroless/java:11
COPY --from=build-hapi /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war
EXPOSE 8080
WORKDIR /app
CMD ["main.war"]
``` ```
Note that distroless images are also automatically build and pushed to the container registry,
see the `-distroless` suffix in the image tags.

260
src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java
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@@ -1,170 +1,186 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer; import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder; import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
import org.apache.commons.lang3.StringUtils; import org.apache.lucene.util.Version;
import org.elasticsearch.action.admin.indices.stats.IndexStats; import org.hibernate.cfg.AvailableSettings;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchBackendSettings;
import org.hibernate.search.backend.elasticsearch.index.IndexStatus; import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings; import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings; import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
import org.hibernate.search.backend.lucene.lowlevel.directory.impl.LocalFileSystemDirectoryProvider;
import org.hibernate.search.engine.cfg.BackendSettings; import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.automaticindexing.session.AutomaticIndexingSynchronizationStrategyNames; import org.hibernate.search.mapper.orm.automaticindexing.session.AutomaticIndexingSynchronizationStrategyNames;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings; import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName; import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
import org.springframework.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy;
import org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy;
import org.springframework.core.env.CompositePropertySource; import org.springframework.core.env.CompositePropertySource;
import org.springframework.core.env.ConfigurableEnvironment; import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.core.env.EnumerablePropertySource; import org.springframework.core.env.EnumerablePropertySource;
import org.springframework.core.env.PropertySource; import org.springframework.core.env.PropertySource;
import java.util.Arrays; import java.util.*;
import java.util.HashMap;
import java.util.Map;
import java.util.Properties;
public class EnvironmentHelper { public class EnvironmentHelper {
public static Properties getHibernateProperties(ConfigurableEnvironment environment) { public static Properties getHibernateProperties(ConfigurableEnvironment environment) {
Properties properties = new Properties(); Properties properties = new Properties();
Map<String, Object> jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties");
for (Map.Entry<String, Object> entry : jpaProps.entrySet()) {
String strippedKey = entry.getKey().replace("spring.jpa.properties.", "");
properties.put(strippedKey, entry.getValue().toString());
}
Map<String, Object> jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties"); //Spring Boot Autoconfiguration defaults
properties.putIfAbsent("hibernate.format_sql", "false"); properties.putIfAbsent(AvailableSettings.SCANNER, "org.hibernate.boot.archive.scan.internal.DisabledScanner");
properties.putIfAbsent("hibernate.show_sql", "false"); properties.putIfAbsent(AvailableSettings.IMPLICIT_NAMING_STRATEGY, SpringImplicitNamingStrategy.class.getName());
properties.putIfAbsent("hibernate.hbm2ddl.auto", "update"); properties.putIfAbsent(AvailableSettings.PHYSICAL_NAMING_STRATEGY, SpringPhysicalNamingStrategy.class.getName());
properties.putIfAbsent("hibernate.jdbc.batch_size", "20"); //TODO The bean factory should be added as parameter but that requires that it can be injected from the entityManagerFactory bean from xBaseConfig
properties.putIfAbsent("hibernate.cache.use_query_cache", "false"); //properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
properties.putIfAbsent("hibernate.cache.use_second_level_cache", "false");
properties.putIfAbsent("hibernate.cache.use_structured_entries", "false");
properties.putIfAbsent("hibernate.cache.use_minimal_puts", "false");
if (jpaProps.getOrDefault("spring.jpa.properties.hibernate.search.enabled", "false").toString() == "true") { //hapi-fhir-jpaserver-base "sensible defaults"
properties.putIfAbsent(HibernateOrmMapperSettings.ENABLED, true); Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean().getJpaPropertyMap();
properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), "local-filesystem"); hapiJpaPropertyMap.forEach(properties::putIfAbsent);
properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
properties.putIfAbsent(BackendSettings.backendKey(BackendSettings.TYPE), "lucene");
properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), "LUCENE_CURRENT");
} else {
properties.putIfAbsent(HibernateOrmMapperSettings.ENABLED, false);
}
for (Map.Entry<String, Object> entry : jpaProps.entrySet()) { //hapi-fhir-jpaserver-starter defaults
String strippedKey = entry.getKey().replace("spring.jpa.properties.", ""); properties.putIfAbsent(AvailableSettings.FORMAT_SQL, false);
properties.put(strippedKey, entry.getValue().toString()); properties.putIfAbsent(AvailableSettings.SHOW_SQL, false);
} properties.putIfAbsent(AvailableSettings.HBM2DDL_AUTO, "update");
properties.putIfAbsent(AvailableSettings.STATEMENT_BATCH_SIZE, 20);
properties.putIfAbsent(AvailableSettings.USE_QUERY_CACHE, false);
properties.putIfAbsent(AvailableSettings.USE_SECOND_LEVEL_CACHE, false);
properties.putIfAbsent(AvailableSettings.USE_STRUCTURED_CACHE, false);
properties.putIfAbsent(AvailableSettings.USE_MINIMAL_PUTS, false);
//Hibernate Search defaults
properties.putIfAbsent(HibernateOrmMapperSettings.ENABLED, false);
if (Boolean.parseBoolean(String.valueOf(properties.get(HibernateOrmMapperSettings.ENABLED)))) {
if (isElasticsearchEnabled(environment)) {
properties.putIfAbsent(BackendSettings.backendKey(BackendSettings.TYPE), ElasticsearchBackendSettings.TYPE_NAME);
} else {
properties.putIfAbsent(BackendSettings.backendKey(BackendSettings.TYPE), LuceneBackendSettings.TYPE_NAME);
}
if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null if (properties.get(BackendSettings.backendKey(BackendSettings.TYPE)).equals(LuceneBackendSettings.TYPE_NAME)) {
&& environment.getProperty("elasticsearch.enabled", Boolean.class) == true) { properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), LocalFileSystemDirectoryProvider.NAME);
ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder(); properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class); properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
if (requiredIndexStatus == null) { properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), Version.LATEST);
builder.setRequiredIndexStatus(IndexStatus.YELLOW);
} else {
builder.setRequiredIndexStatus(requiredIndexStatus);
}
builder.setRestUrl(getElasticsearchServerUrl(environment)); } else if (properties.get(BackendSettings.backendKey(BackendSettings.TYPE)).equals(ElasticsearchBackendSettings.TYPE_NAME)) {
builder.setUsername(getElasticsearchServerUsername(environment)); ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
builder.setPassword(getElasticsearchServerPassword(environment)); IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
builder.setProtocol(getElasticsearchServerProtocol(environment)); builder.setRequiredIndexStatus(requireNonNullElse(requiredIndexStatus, IndexStatus.YELLOW));
SchemaManagementStrategyName indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", SchemaManagementStrategyName.class); builder.setRestUrl(getElasticsearchServerUrl(environment));
if (indexSchemaManagementStrategy == null) { builder.setUsername(getElasticsearchServerUsername(environment));
builder.setIndexSchemaManagementStrategy(SchemaManagementStrategyName.CREATE); builder.setPassword(getElasticsearchServerPassword(environment));
} else { builder.setProtocol(getElasticsearchServerProtocol(environment));
builder.setIndexSchemaManagementStrategy(indexSchemaManagementStrategy); SchemaManagementStrategyName indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", SchemaManagementStrategyName.class);
} builder.setIndexSchemaManagementStrategy(requireNonNullElse(indexSchemaManagementStrategy, SchemaManagementStrategyName.CREATE));
// pretty_print_json_log: false Boolean refreshAfterWrite = environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class);
Boolean refreshAfterWrite = environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class); if (refreshAfterWrite == null || !refreshAfterWrite) {
if (refreshAfterWrite == null || refreshAfterWrite == false) { builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.ASYNC);
builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.ASYNC); } else {
} else { builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.READ_SYNC);
builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.READ_SYNC); }
} builder.setDebugPrettyPrintJsonLog(requireNonNullElse(environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class), false));
// pretty_print_json_log: false builder.apply(properties);
Boolean prettyPrintJsonLog = environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class);
if (prettyPrintJsonLog == null) {
builder.setDebugPrettyPrintJsonLog(false);
} else {
builder.setDebugPrettyPrintJsonLog(prettyPrintJsonLog);
}
builder.apply(properties);
}
return properties;
}
public static String getElasticsearchServerUrl(ConfigurableEnvironment environment) { } else {
return environment.getProperty("elasticsearch.rest_url", String.class); throw new UnsupportedOperationException("Unsupported Hibernate Search backend: " + properties.get(BackendSettings.backendKey(BackendSettings.TYPE)));
} }
}
return properties;
}
//TODO Removed when we're up on Java 11
private static <T> T requireNonNullElse(T obj, T defaultObj) {
return (obj != null) ? obj : requireNonNull(defaultObj, "defaultObj");
}
//TODO Removed when we're up on Java 11
private static <T> T requireNonNull(T obj, String message) {
if (obj == null)
throw new NullPointerException(message);
return obj;
}
public static String getElasticsearchServerUrl(ConfigurableEnvironment environment) {
return environment.getProperty("elasticsearch.rest_url", String.class);
}
public static String getElasticsearchServerProtocol(ConfigurableEnvironment environment) { public static String getElasticsearchServerProtocol(ConfigurableEnvironment environment) {
return environment.getProperty("elasticsearch.protocol", String.class, "http"); return environment.getProperty("elasticsearch.protocol", String.class, "http");
} }
public static String getElasticsearchServerUsername(ConfigurableEnvironment environment) { public static String getElasticsearchServerUsername(ConfigurableEnvironment environment) {
return environment.getProperty("elasticsearch.username"); return environment.getProperty("elasticsearch.username");
} }
public static String getElasticsearchServerPassword(ConfigurableEnvironment environment) { public static String getElasticsearchServerPassword(ConfigurableEnvironment environment) {
return environment.getProperty("elasticsearch.password"); return environment.getProperty("elasticsearch.password");
} }
public static Boolean isElasticsearchEnabled(ConfigurableEnvironment environment) { public static Boolean isElasticsearchEnabled(ConfigurableEnvironment environment) {
if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null) { if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null) {
return environment.getProperty("elasticsearch.enabled", Boolean.class); return environment.getProperty("elasticsearch.enabled", Boolean.class);
} else { } else {
return false; return false;
} }
} }
public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv, public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv,
String aKeyPrefix) { String aKeyPrefix) {
Map<String, Object> result = new HashMap<>(); Map<String, Object> result = new HashMap<>();
Map<String, Object> map = getAllProperties(aEnv); Map<String, Object> map = getAllProperties(aEnv);
for (Map.Entry<String, Object> entry : map.entrySet()) { for (Map.Entry<String, Object> entry : map.entrySet()) {
String key = entry.getKey(); String key = entry.getKey();
if (key.startsWith(aKeyPrefix)) { if (key.startsWith(aKeyPrefix)) {
result.put(key, entry.getValue()); result.put(key, entry.getValue());
} }
} }
return result; return result;
} }
public static Map<String, Object> getAllProperties(ConfigurableEnvironment aEnv) { public static Map<String, Object> getAllProperties(ConfigurableEnvironment aEnv) {
Map<String, Object> result = new HashMap<>(); Map<String, Object> result = new HashMap<>();
aEnv.getPropertySources().forEach(ps -> addAll(result, getAllProperties(ps))); aEnv.getPropertySources().forEach(ps -> addAll(result, getAllProperties(ps)));
return result; return result;
} }
public static Map<String, Object> getAllProperties(PropertySource<?> aPropSource) { public static Map<String, Object> getAllProperties(PropertySource<?> aPropSource) {
Map<String, Object> result = new HashMap<>(); Map<String, Object> result = new HashMap<>();
if (aPropSource instanceof CompositePropertySource) { if (aPropSource instanceof CompositePropertySource) {
CompositePropertySource cps = (CompositePropertySource) aPropSource; CompositePropertySource cps = (CompositePropertySource) aPropSource;
cps.getPropertySources().forEach(ps -> addAll(result, getAllProperties(ps))); cps.getPropertySources().forEach(ps -> addAll(result, getAllProperties(ps)));
return result; return result;
} }
if (aPropSource instanceof EnumerablePropertySource<?>) { if (aPropSource instanceof EnumerablePropertySource<?>) {
EnumerablePropertySource<?> ps = (EnumerablePropertySource<?>) aPropSource; EnumerablePropertySource<?> ps = (EnumerablePropertySource<?>) aPropSource;
Arrays.asList(ps.getPropertyNames()).forEach(key -> result.put(key, ps.getProperty(key))); Arrays.asList(ps.getPropertyNames()).forEach(key -> result.put(key, ps.getProperty(key)));
return result; return result;
} }
return result; return result;
} }
private static void addAll(Map<String, Object> aBase, Map<String, Object> aToBeAdded) { private static void addAll(Map<String, Object> aBase, Map<String, Object> aToBeAdded) {
for (Map.Entry<String, Object> entry : aToBeAdded.entrySet()) { for (Map.Entry<String, Object> entry : aToBeAdded.entrySet()) {
if (aBase.containsKey(entry.getKey())) { if (aBase.containsKey(entry.getKey())) {
continue; continue;
} }
aBase.put(entry.getKey(), entry.getValue()); aBase.put(entry.getKey(), entry.getValue());
} }
} }
} }