Personal-Twin/hapi-fhir-jpaserver-starter
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Merge remote-tracking branch 'origin/master' into ja_20231203_hapi_7_0

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This commit is contained in:
dotasek.dev
2024-02-27 14:37:31 -05:00
parent 164e0a98c9 9e21d8062e
commit eae61fd68a
27 changed files with 362 additions and 182 deletions
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12
.github/workflows/chart-test.yaml vendored
View File

@@ -10,7 +10,7 @@ on:
jobs:
lint:
runs-on: ubuntu-22.04
container: quay.io/helmpack/chart-testing:v3.8.0@sha256:f058c660a28d99a9394ae081d98921efe068079531f247c86b8054e3c9d407aa
container: quay.io/helmpack/chart-testing:v3.10.1@sha256:7d8a7f99fc5840142249cc33ed6d9752fc66b92f9e1bf792d987ee85227d84da
steps:
- name: Install helm-docs
working-directory: /tmp
@@ -27,7 +27,7 @@ jobs:
git config --global --add safe.directory /__w/hapi-fhir-jpaserver-starter/hapi-fhir-jpaserver-starter
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
fetch-depth: 0
@@ -41,17 +41,17 @@ jobs:
runs-on: ubuntu-22.04
strategy:
matrix:
k8s-version: [1.25.9, 1.26.4, 1.27.2]
k8s-version: [1.25.11, 1.26.6, 1.27.3, 1.28.0, 1.29.0]
needs:
- lint
steps:
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
with:
fetch-depth: 0
- name: Set up chart-testing
uses: helm/chart-testing-action@e8788873172cb653a90ca2e819d79d65a66d4e76 # v2.4.0
uses: helm/chart-testing-action@e6669bcd63d7cb57cb4380c33043eebe5d111992 # v2.6.1
- name: Run chart-testing (list-changed)
id: list-changed
@@ -62,7 +62,7 @@ jobs:
fi
- name: Create k8s Kind Cluster
uses: helm/kind-action@fa81e57adff234b2908110485695db0f181f3c67 # v1.7.0
uses: helm/kind-action@dda0770415bac9fc20092cacbc54aa298604d140 # v1.8.0
if: ${{ steps.list-changed.outputs.changed == 'true' }}
with:
cluster_name: kind-cluster-k8s-${{ matrix.k8s-version }}

6
charts/hapi-fhir-jpaserver/Chart.lock
View File

@@ -1,6 +1,6 @@
dependencies:
- name: postgresql
repository: oci://registry-1.docker.io/bitnamicharts
version: 12.5.6
digest: sha256:4d21dbc02bbdb55b957b0093e37376853727de82396abfadfaf1d738bd51b8e6
generated: "2023-06-03T20:58:45.922102213+02:00"
version: 13.2.27
digest: sha256:6374f6f32d32adbe6763c48e2d817d85ec20a1784b2aea1fb0312c658f8e58e9
generated: "2024-01-10T17:56:36.521957926+01:00"

26
charts/hapi-fhir-jpaserver/Chart.yaml
View File

@@ -7,21 +7,25 @@ sources:
- https://github.com/hapifhir/hapi-fhir-jpaserver-starter
dependencies:
- name: postgresql
version: 12.5.6
version: 13.2.27
repository: oci://registry-1.docker.io/bitnamicharts
condition: postgresql.enabled
appVersion: 6.8.3
version: 0.14.0
appVersion: 6.10.1
version: 0.15.0
annotations:
artifacthub.io/license: Apache-2.0
artifacthub.io/containsSecurityUpdates: "false"
artifacthub.io/operator: "false"
artifacthub.io/prerelease: "false"
artifacthub.io/recommendations: |
- url: https://artifacthub.io/packages/helm/prometheus-community/kube-prometheus-stack
- url: https://artifacthub.io/packages/helm/bitnami/postgresql
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: updated starter image to 6.8.3
- kind: fixed
description: incorrect handling of existing secret database config
- kind: added
description: support for using a non-admin user for the postgres database
- kind: added
description: ability to create a dedicated ServiceAccount
- kind: changed
description: updated starter image to 6.10.1
- kind: changed
description: updated curlimages/curl to 8.5.0
- kind: changed
description: "updated postgresql sub-chart to 13.2.27. ⚠️: this updates the used PostgreSQL image from v15 to v16."

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

@@ -1,6 +1,6 @@
# HAPI FHIR JPA Server Starter Helm Chart
![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)
![Version: 0.15.0](https://img.shields.io/badge/Version-0.15.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 6.10.1](https://img.shields.io/badge/AppVersion-6.10.1-informational?style=flat-square)
This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
@@ -15,7 +15,7 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| Repository | Name | Version |
|------------|------|---------|
| oci://registry-1.docker.io/bitnamicharts | postgresql | 12.5.6 |
| oci://registry-1.docker.io/bitnamicharts | postgresql | 13.2.27 |
## Values
@@ -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 | `"v6.8.3@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. |
| image.tag | string | `"v6.10.1@sha256:4eac1b3481180b028616d1fab7e657e368538063d75f7ed3be2032e34c657dd4"` | 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 |
@@ -57,10 +57,6 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| postgresql.auth.database | string | `"fhir"` | name for a custom database to create |
| postgresql.auth.existingSecret | string | `""` | Name of existing secret to use for PostgreSQL credentials `auth.postgresPassword`, `auth.password`, and `auth.replicationPassword` will be ignored and picked up from this secret The secret must contain the keys `postgres-password` (which is the password for "postgres" admin user), `password` (which is the password for the custom user to create when `auth.username` is set), and `replication-password` (which is the password for replication user). The secret might also contains the key `ldap-password` if LDAP is enabled. `ldap.bind_password` will be ignored and picked from this secret in this case. The value is evaluated as a template. |
| postgresql.enabled | bool | `true` | enable an included PostgreSQL DB. see <https://github.com/bitnami/charts/tree/master/bitnami/postgresql> for details if set to `false`, the values under `externalDatabase` are used |
| postgresql.primary.containerSecurityContext.allowPrivilegeEscalation | bool | `false` | |
| postgresql.primary.containerSecurityContext.capabilities.drop[0] | string | `"ALL"` | |
| postgresql.primary.containerSecurityContext.runAsNonRoot | bool | `true` | |
| postgresql.primary.containerSecurityContext.seccompProfile.type | string | `"RuntimeDefault"` | |
| replicaCount | int | `1` | number of replicas to deploy |
| resources | object | `{}` | configure the FHIR server's resource requests and limits |
| securityContext.allowPrivilegeEscalation | bool | `false` | |

2
charts/hapi-fhir-jpaserver/templates/deployment.yaml
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@@ -31,7 +31,7 @@ spec:
{{- toYaml .Values.podSecurityContext | nindent 8 }}
initContainers:
- name: wait-for-db-to-be-ready
image: docker.io/bitnami/postgresql:15.3.0-debian-11-r7@sha256:cc301eef743685f4f69d1d719853988e8a9650c90fd9521f4742ce400b3fdf6a
image: docker.io/bitnami/postgresql:16.1.0-debian-11-r18@sha256:06f1f2297f6241a02bd8e8c025b31625254ca66784ac75a4a62e945fa611d045
imagePullPolicy: IfNotPresent
{{- with .Values.restrictedContainerSecurityContext }}
securityContext:

13
charts/hapi-fhir-jpaserver/values.yaml
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@@ -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: "v6.8.3@sha256:6195f1116ebabfb0a608addde043b3e524c456c4d4f35b3d25025afd7dcd2e27"
tag: "v6.10.1@sha256:4eac1b3481180b028616d1fab7e657e368538063d75f7ed3be2032e34c657dd4"
# -- image pullPolicy to use
pullPolicy: IfNotPresent
@@ -121,15 +121,6 @@ postgresql:
# picked from this secret in this case.
# The value is evaluated as a template.
existingSecret: ""
primary:
containerSecurityContext:
allowPrivilegeEscalation: false
capabilities:
drop:
- ALL
runAsNonRoot: true
seccompProfile:
type: RuntimeDefault
# -- readiness probe
# @ignored
@@ -240,7 +231,7 @@ curl:
image:
registry: docker.io
repository: curlimages/curl
tag: 8.4.0@sha256:4a3396ae573c44932d06ba33f8696db4429c419da87cbdc82965ee96a37dd0af
tag: 8.6.0@sha256:c3b8bee303c6c6beed656cfc921218c529d65aa61114eb9e27c62047a1271b9b
tests:
# -- configure the test pods resource requests and limits

3
configs/app/index.html Normal file
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@@ -0,0 +1,3 @@
<p>
Greetings from the custom web app page!
</p>

14
custom/about.html Normal file
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@@ -0,0 +1,14 @@
<p>
<b>This is a custom about page! It means you have configured 'custom_content_path: ./custom' in the application.yaml</b>
</p>
<p>
This server provides a complete implementation of the FHIR Specification
using a 100% open source software stack.
</p>
<p>
This server is built
from a number of modules of the
<a href="https://github.com/hapifhir/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>

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14
custom/welcome.html Normal file
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@@ -0,0 +1,14 @@
<p>
<b>This is a custom welcome page! It means you have configured 'custom_content_path: ./custom' in the application.yaml</b>
</p>
<p>
This server provides a complete implementation of the FHIR Specification
using a 100% open source software stack.
</p>
<p>
This server is built
from a number of modules of the
<a href="https://github.com/hapifhir/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>

41
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
View File

@@ -79,9 +79,8 @@ public class AppProperties {
private Boolean install_transitive_ig_dependencies = true;
private Map<String, PackageInstallationSpec> implementationGuides = null;
private String staticLocation = null;
private String staticLocationPrefix = "/static";
private String custom_content_path = null;
private String app_content_path = null;
private Boolean lastn_enabled = false;
private boolean store_resource_in_lucene_index_enabled = false;
@@ -94,16 +93,9 @@ public class AppProperties {
private Integer bundle_batch_pool_max_size = 100;
private final Set<String> local_base_urls = new HashSet<>();
private final Set<String> logical_urls = new HashSet<>();
private final List<String> custom_interceptor_classes = new ArrayList<>();
public String getStaticLocationPrefix() {
return staticLocationPrefix;
}
public void setStaticLocationPrefix(String staticLocationPrefix) {
this.staticLocationPrefix = staticLocationPrefix;
}
public List<String> getCustomInterceptorClasses() {
@@ -111,14 +103,6 @@ public class AppProperties {
}
public String getStaticLocation() {
return staticLocation;
}
public void setStaticLocation(String staticLocation) {
this.staticLocation = staticLocation;
}
public Boolean getOpenapi_enabled() {
return openapi_enabled;
@@ -575,7 +559,7 @@ public Cors getCors() {
public void setInstall_transitive_ig_dependencies(boolean install_transitive_ig_dependencies) {
this.install_transitive_ig_dependencies = install_transitive_ig_dependencies;
}
public Integer getBundle_batch_pool_size() {
return this.bundle_batch_pool_size;
}
@@ -600,6 +584,7 @@ public Cors getCors() {
return logical_urls;
}
public Boolean getIg_runtime_upload_enabled() {
return ig_runtime_upload_enabled;
}
@@ -608,6 +593,22 @@ public Cors getCors() {
this.ig_runtime_upload_enabled = ig_runtime_upload_enabled;
}
public String getCustom_content_path() {
return custom_content_path;
}
public void setCustom_content_path(String custom_content_path) {
this.custom_content_path = custom_content_path;
}
public String getApp_content_path() {
return app_content_path;
}
public void setApp_content_path(String app_content_path) {
this.app_content_path = app_content_path;
}
public static class Cors {
private Boolean allow_Credentials = true;
private List<String> allowed_origin = List.of("*");

50
src/main/java/ca/uhn/fhir/jpa/starter/ExtraStaticFilesConfigurer.java
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@@ -1,50 +0,0 @@
package ca.uhn.fhir.jpa.starter;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.Ordered;
import org.springframework.web.servlet.config.annotation.ResourceHandlerRegistry;
import org.springframework.web.servlet.config.annotation.ViewControllerRegistry;
import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
import java.net.URI;
@Configuration
@ConditionalOnProperty(prefix = "hapi.fhir", name = "staticLocation")
public class ExtraStaticFilesConfigurer implements WebMvcConfigurer {
private String staticLocation;
private String rootContextPath;
public ExtraStaticFilesConfigurer(AppProperties appProperties) {
rootContextPath = appProperties.getStaticLocationPrefix();
if (rootContextPath.endsWith("/"))
rootContextPath = rootContextPath.substring(0, rootContextPath.lastIndexOf('/'));
staticLocation = appProperties.getStaticLocation();
if (staticLocation.endsWith("/")) staticLocation = staticLocation.substring(0, staticLocation.lastIndexOf('/'));
}
@Override
public void addResourceHandlers(ResourceHandlerRegistry theRegistry) {
theRegistry.addResourceHandler(rootContextPath + "/**").addResourceLocations(staticLocation);
}
@Override
public void addViewControllers(ViewControllerRegistry registry) {
String path = URI.create(staticLocation).getPath();
String lastSegment = path.substring(path.lastIndexOf('/') + 1);
registry.addViewController(rootContextPath)
.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
registry.addViewController(rootContextPath + "/*")
.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
registry.addViewController(rootContextPath + "/" + lastSegment + "/")
.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
registry.setOrder(Ordered.HIGHEST_PRECEDENCE);
}
}

3
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfig.java
View File

@@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.to.FhirTesterMvcConfig;
import ca.uhn.fhir.to.TesterConfig;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@@ -18,7 +19,7 @@ import org.springframework.context.annotation.Import;
*/
@Configuration
@Import(FhirTesterMvcConfig.class)
// @Conditional(FhirTesterConfigCondition.class)
@Conditional(FhirTesterConfigCondition.class)
public class FhirTesterConfig {
/**

4
src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java
View File

@@ -44,6 +44,7 @@ import ca.uhn.fhir.jpa.starter.annotations.OnImplementationGuidesPresent;
import ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory;
import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
@@ -272,8 +273,7 @@ public class StarterJpaConfig {
IPackageInstallerSvc packageInstallerSvc,
ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc,
ApplicationContext appContext,
Optional<IpsOperationProvider> theIpsOperationProvider,
Optional<IImplementationGuideOperationProvider> implementationGuideOperationProvider) {
Optional<IpsOperationProvider> theIpsOperationProvider, Optional<IImplementationGuideOperationProvider> implementationGuideOperationProvider) {
RestfulServer fhirServer = new RestfulServer(fhirSystemDao.getContext());
List<String> supportedResourceTypes = appProperties.getSupported_resource_types();

2
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryDstu3.java
View File

@@ -47,7 +47,7 @@ public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryV
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(
new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
new SearchParameterMap().setLoadSynchronous(true).add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size()).stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));

2
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR4.java
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@@ -48,7 +48,7 @@ public class RepositoryValidationInterceptorFactoryR4 implements IRepositoryVali
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(
new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
new SearchParameterMap().setLoadSynchronous(true).add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));

2
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR4B.java
View File

@@ -48,7 +48,7 @@ public class RepositoryValidationInterceptorFactoryR4B implements IRepositoryVal
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(
new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
new SearchParameterMap().setLoadSynchronous(true).add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));

2
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR5.java
View File

@@ -47,7 +47,7 @@ public class RepositoryValidationInterceptorFactoryR5 implements IRepositoryVali
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(
new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
new SearchParameterMap().setLoadSynchronous(true).add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));

12
src/main/java/ca/uhn/fhir/jpa/starter/ig/IImplementationGuideOperationProvider.java
View File

@@ -9,16 +9,10 @@ import java.io.IOException;
public interface IImplementationGuideOperationProvider {
static PackageInstallationSpec toPackageInstallationSpec(byte[] npmPackageAsByteArray) throws IOException {
NpmPackage npmPackage = NpmPackage.fromPackage(new ByteArrayInputStream(npmPackageAsByteArray));
return new PackageInstallationSpec()
.setName(npmPackage.name())
.setPackageContents(npmPackageAsByteArray)
.setVersion(npmPackage.version())
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL)
.setFetchDependencies(false);
return new PackageInstallationSpec().setName(npmPackage.name()).setPackageContents(npmPackageAsByteArray).setVersion(npmPackage.version()).setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL).setFetchDependencies(false);
}
// The following declaration is the one that counts but cannot be used across different versions as stating
// Base64BinaryType would bind to a separate version
// @Operation(name = "$install", typeName = "ImplementationGuide")
// The following declaration is the one that counts but cannot be used across different versions as stating Base64BinaryType would bind to a separate version
// Parameters install(@OperationParam(name = "npmContent",min = 1, max = 1) Base64BinaryType implementationGuide);
// Parameters uninstall(@OperationParam(name = "name", min = 1, max = 1) String name, @OperationParam(name = "version", min = 1, max = 1) String version) ;
}

15
src/main/java/ca/uhn/fhir/jpa/starter/ig/ImplementationGuideR4OperationProvider.java
View File

@@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.starter.ig;
import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
@@ -22,15 +23,21 @@ public class ImplementationGuideR4OperationProvider implements IImplementationGu
}
@Operation(name = "$install", typeName = "ImplementationGuide")
public Parameters install(
@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
public Parameters install(@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
try {
packageInstallerSvc.install(
IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
packageInstallerSvc.install(IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
} catch (IOException e) {
throw new RuntimeException(e);
}
return new Parameters();
}
@Operation(name = "$uninstall", typeName = "ImplementationGuide")
public Parameters uninstall(@OperationParam(name = "name", min = 1, max = 1) String name, @OperationParam(name = "version", min = 1, max = 1) String version) {
packageInstallerSvc.uninstall(new PackageInstallationSpec().setName(name).setVersion(version));
return new Parameters();
}
}

17
src/main/java/ca/uhn/fhir/jpa/starter/ig/ImplementationGuideR5OperationProvider.java
View File

@@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.starter.ig;
import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
@@ -13,7 +14,7 @@ import java.io.IOException;
@Conditional({OnR5Condition.class, IgConfigCondition.class})
@Service
public class ImplementationGuideR5OperationProvider {
public class ImplementationGuideR5OperationProvider implements IImplementationGuideOperationProvider {
IPackageInstallerSvc packageInstallerSvc;
@@ -22,15 +23,21 @@ public class ImplementationGuideR5OperationProvider {
}
@Operation(name = "$install", typeName = "ImplementationGuide")
public Parameters install(
@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
public Parameters install(@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
try {
packageInstallerSvc.install(
IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
packageInstallerSvc.install(IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
} catch (IOException e) {
throw new RuntimeException(e);
}
return new Parameters();
}
@Operation(name = "$uninstall", typeName = "ImplementationGuide")
public org.hl7.fhir.r4.model.Parameters uninstall(@OperationParam(name = "name", min = 1, max = 1) String name, @OperationParam(name = "version", min = 1, max = 1) String version) {
packageInstallerSvc.uninstall(new PackageInstallationSpec().setName(name).setVersion(version));
return new org.hl7.fhir.r4.model.Parameters();
}
}

40
src/main/java/ca/uhn/fhir/jpa/starter/web/CustomContentFilesConfigurer.java Normal file
View File

@@ -0,0 +1,40 @@
package ca.uhn.fhir.jpa.starter.web;
import ca.uhn.fhir.jpa.starter.AppProperties;
import org.jetbrains.annotations.NotNull;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.io.FileUrlResource;
import org.springframework.web.servlet.config.annotation.ResourceHandlerRegistry;
import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
import java.net.MalformedURLException;
@Configuration
@ConditionalOnProperty(prefix = "hapi.fhir", name = "custom_content_path")
public class CustomContentFilesConfigurer implements WebMvcConfigurer {
public static final String CUSTOM_CONTENT = "/content";
private String customContentPath;
public CustomContentFilesConfigurer(AppProperties appProperties) {
customContentPath = appProperties.getCustom_content_path();
if (customContentPath.endsWith("/"))
customContentPath = customContentPath.substring(0, customContentPath.lastIndexOf('/'));
}
@Override
public void addResourceHandlers(@NotNull ResourceHandlerRegistry theRegistry) {
if (!theRegistry.hasMappingForPattern(CUSTOM_CONTENT + "/**")) {
try {
theRegistry.addResourceHandler(CUSTOM_CONTENT + "/**").addResourceLocations(new FileUrlResource(customContentPath));
} catch (MalformedURLException e) {
throw new RuntimeException(e);
}
}
}
}

56
src/main/java/ca/uhn/fhir/jpa/starter/web/WebAppFilesConfigurer.java Normal file
View File

@@ -0,0 +1,56 @@
package ca.uhn.fhir.jpa.starter.web;
import ca.uhn.fhir.jpa.starter.AppProperties;
import org.jetbrains.annotations.NotNull;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.Ordered;
import org.springframework.core.io.FileUrlResource;
import org.springframework.web.servlet.config.annotation.ResourceHandlerRegistry;
import org.springframework.web.servlet.config.annotation.ViewControllerRegistry;
import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
import java.net.MalformedURLException;
import java.net.URI;
@Configuration
@ConditionalOnProperty(prefix = "hapi.fhir", name = "app_content_path")
public class WebAppFilesConfigurer implements WebMvcConfigurer {
public static final String WEB_CONTENT = "web";
private String appContentPath;
public WebAppFilesConfigurer(AppProperties appProperties) {
appContentPath = appProperties.getApp_content_path();
if (appContentPath.endsWith("/"))
appContentPath = appContentPath.substring(0, appContentPath.lastIndexOf('/'));
}
@Override
public void addResourceHandlers(@NotNull ResourceHandlerRegistry theRegistry) {
if (!theRegistry.hasMappingForPattern(WEB_CONTENT + "/**")) {
{
try {
theRegistry.addResourceHandler(WEB_CONTENT + "/**").addResourceLocations(new FileUrlResource(appContentPath));
} catch (MalformedURLException e) {
throw new RuntimeException(e);
}
}
}
}
@Override
public void addViewControllers(@NotNull ViewControllerRegistry registry) {
String path = URI.create(appContentPath).getPath();
String lastSegment = path.substring(path.lastIndexOf('/') + 1);
registry.addViewController(WEB_CONTENT + "/" + lastSegment).setViewName("redirect:" + lastSegment + "/index.html");
registry.addViewController(WEB_CONTENT + "/" + lastSegment + "/").setViewName("redirect:index.html");
registry.setOrder(Ordered.HIGHEST_PRECEDENCE);
}
}

14
src/main/resources/application.yaml
View File

@@ -14,8 +14,8 @@ spring:
check-location: false
baselineOnMigrate: true
datasource:
url: 'jdbc:h2:file:./target/database/h2'
#url: jdbc:h2:mem:test_mem
#url: 'jdbc:h2:file:./target/database/h2'
url: jdbc:h2:mem:test_mem
username: sa
password: null
driverClassName: org.h2.Driver
@@ -76,10 +76,12 @@ hapi:
### forces the use of the https:// protocol for the returned server address.
### alternatively, it may be set using the X-Forwarded-Proto header.
# use_apache_address_strategy_https: false
### enables the server to host content like HTML, css, etc. under the url pattern of eg. /static/**
# staticLocationPrefix: /static
### the deepest folder level will be used. E.g. - if you put file:/foo/bar/bazz as value then the files are resolved under /static/bazz/**
#staticLocation: file:/foo/bar/bazz
### enables the server to overwrite defaults on HTML, css, etc. under the url pattern of eg. /content/custom **
### Folder with custom content MUST be named custom. If omitted then default content applies
#custom_content_path: ./custom
### enables the server host custom content. If e.g. the value ./configs/app is supplied then the content
### will be served under /web/app
#app_content_path: ./configs/app
### enable to set the Server URL
# server_address: http://hapi.fhir.org/baseR4
# defer_indexing_for_codesystems_of_size: 101

65
src/main/webapp/WEB-INF/templates/about.html
View File

@@ -21,21 +21,23 @@
<h3 class="panel-title">About This Server</h3>
</div>
<div class="panel-body">
<p>
This server provides a complete implementation of the FHIR Specification
using a 100% open source software stack.
</p>
<p>
This server is built
from a number of modules of the
<a href="https://github.com/jamesagnew/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>
<p>
<div id="replacementAbout">
<p>
This server provides a complete implementation of the FHIR Specification
using a 100% open source software stack.
</p>
<p>
This server is built
from a number of modules of the
<a href="https://github.com/hapifhir/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>
</p>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
@@ -55,6 +57,41 @@
</div>
<div th:replace="tmpl-footer :: footer"></div>
</form>
</form>
</body>
</html>
<script>
// Function to check if a file exists using AJAX
function fileExists(filePath, callback) {
var xhr = new XMLHttpRequest();
xhr.onreadystatechange = function() {
if (xhr.readyState === 4) {
callback(xhr.status === 200);
}
};
xhr.open("HEAD", filePath, true);
xhr.send();
}
// Replace content if the replacement exists
fileExists("content/custom/about.html", function(exists) {
if (exists) {
loadFile("content/custom/about.html", function(content) {
var replacementContainer = document.getElementById("replacementAbout");
replacementContainer.innerHTML = content;
});
}
});
// Function to load file content using AJAX
function loadFile(filePath, callback) {
var xhr = new XMLHttpRequest();
xhr.onreadystatechange = function() {
if (xhr.readyState === 4 && xhr.status === 200) {
callback(xhr.responseText);
}
};
xhr.open("GET", filePath, true);
xhr.send();
}
</script>

51
src/main/webapp/WEB-INF/templates/tmpl-banner.html
View File

@@ -1,20 +1,41 @@
<!DOCTYPE html>
<html lang="en">
<div th:fragment="banner">
<div class="row">
<div class="col-md-8">
<img src="img/sample-logo.jpg" width="383" alt="Sample Logo" />
</div>
<div class="col-md-4">
<img src="img/hapi_fhir_banner_right.png" align="right" />
</div>
</div>
<!-- Error banner in case anything went wrong -->
<div class="alert alert-danger alert-dismissable" th:if="${errorMsg} != null">
<strong>Warning!</strong>
<p th:text="${errorMsg}"></p>
</div>
<div class="row">
<div class="col-md-8">
<img id="logo" src="img/sample-logo.jpg" width="383" alt="Sample Logo"/>
</div>
<div class="col-md-4">
<img src="img/hapi_fhir_banner_right.png" align="right"/>
</div>
</div>
<script>
const customlogoImageUrl = "content/custom/logo.jpg"; // Custom logo
const defaultLogoImageUrl = "img/sample-logo.jpg"; // Default logo
const logoImageElement = document.getElementById("logo");
// Check if the logo image is available
const logoImg = new Image();
logoImg.src = customlogoImageUrl;
logoImg.onload = function() {
// Logo image is available
logoImageElement.src = customlogoImageUrl;
};
logoImg.onerror = function() {
// Logo image is not available, use the default logo image
logoImageElement.src = defaultLogoImageUrl;
};
</script>
<!-- Error banner in case anything went wrong -->
<div class="alert alert-danger alert-dismissable" th:if="${errorMsg} != null">
<strong>Warning!</strong>
<p th:text="${errorMsg}"></p>
</div>
</div>
</html>

68
src/main/webapp/WEB-INF/templates/tmpl-home-welcome.html
View File

@@ -1,16 +1,58 @@
<!DOCTYPE html>
<html lang="en">
<div th:fragment="banner" class="well">
<p>
This server provides a complete implementation of the FHIR Specification
using a 100% open source software stack.
</p>
<p>
This server is built
from a number of modules of the
<a href="https://github.com/jamesagnew/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>
<div th:fragment="banner" class="well" >
<script>
console.log('Hello')
// Function to check if a file exists using AJAX
function fileExists(filePath, callback) {
var xhr = new XMLHttpRequest();
xhr.onreadystatechange = function() {
if (xhr.readyState === 4) {
callback(xhr.status === 200);
}
};
xhr.open("HEAD", filePath, true);
xhr.send();
}
// Replace content if static/welcome.html exists
fileExists("content/custom/welcome.html", function(exists) {
if (exists) {
loadFile("content/custom/welcome.html", function(content) {
var replacementContainer = document.getElementById("replacementWelcome");
replacementContainer.innerHTML = content;
});
}
});
// Function to load file content using AJAX
function loadFile(filePath, callback) {
var xhr = new XMLHttpRequest();
xhr.onreadystatechange = function() {
if (xhr.readyState === 4 && xhr.status === 200) {
callback(xhr.responseText);
}
};
xhr.open("GET", filePath, true);
xhr.send();
}
</script>
<div class="panel-body">
<div id="replacementWelcome">
<p>
This server provides a complete implementation of the FHIR Specification
using a 100% open source software stack.
</p>
<p>
This server is built
from a number of modules of the
<a href="https://github.com/hapifhir/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>
</div>
</div>
</div>
</html>
</html>