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Refactoring
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@jkiddo
jkiddo committed May 28, 2023
1 parent 7789218 commit d720d6b
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Showing 2 changed files with 67 additions and 113 deletions.
5 changes: 2 additions & 3 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.7.11</version>
<version>2.7.12</version>
</parent>

<groupId>org.jkiddo</groupId>
Expand All @@ -26,7 +26,7 @@
<properties>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<hapi_version>6.4.4</hapi_version>
<hapi_version>6.6.0</hapi_version>
</properties>

<dependencies>
Expand All @@ -47,7 +47,6 @@
<version>${hapi_version}</version>
</dependency>

<!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
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175 changes: 65 additions & 110 deletions src/main/java/dk/jkiddo/EmberApplication.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,12 @@

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.packages.loader.PackageLoaderSvc;
import ca.uhn.fhir.rest.client.api.IRestfulClientFactory;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.BundleBuilder;
import com.google.common.base.Strings;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.conn.HttpClientConnectionManager;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.BasicHttpClientConnectionManager;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.IPackageCacheManager;
Expand All @@ -34,15 +27,11 @@
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Random;
import java.util.Objects;
import java.util.concurrent.TimeUnit;
import java.util.function.Function;
import java.util.function.Predicate;
Expand All @@ -51,7 +40,7 @@

import static org.awaitility.Awaitility.await;

@SpringBootApplication(exclude = {DataSourceAutoConfiguration.class, SwaggerConfig.class, ElasticsearchRestClientAutoConfiguration.class })
@SpringBootApplication(exclude = {DataSourceAutoConfiguration.class, SwaggerConfig.class, ElasticsearchRestClientAutoConfiguration.class})
public class EmberApplication implements ApplicationRunner {

public static final String PACKAGE_EXAMPLE = "package/example";
Expand All @@ -77,50 +66,64 @@ public class EmberApplication implements ApplicationRunner {


public static void main(String[] args) {
LOG.info("STARTING THE APPLICATION");
LOG.info("STARTING EMBER");
SpringApplication.run(EmberApplication.class, args);
LOG.info("APPLICATION FINISHED");
LOG.info("ENDING EMBER");
}

@Override
public void run(ApplicationArguments args) throws Exception {

if (!Strings.isNullOrEmpty(directory)) {
loadFilesFromDirectory(directory);
System.exit(1);
}
IBaseBundle resultingExampleBundle;

if (!Strings.isNullOrEmpty(directory))
resultingExampleBundle = loadResourcesFromDirectory(new File(directory));
else
resultingExampleBundle = loadResourcesFromNPM();

emitBundle(resultingExampleBundle);
System.exit(0);
}

@NotNull
private IBaseBundle loadResourcesFromDirectory(File directory) {

var fhirContext = FhirContext.forR5();

List<IBaseResource> resources = Stream.of(Objects.requireNonNull(directory.listFiles())).filter(file -> !file.isDirectory()).filter(file -> file.getName().endsWith(".json")).filter(file -> file.getName().contains("mplementation")).map(f -> {
try {
return new String(Files.readAllBytes(Path.of(f.getPath())));
} catch (IOException e) {
throw new RuntimeException(e.getMessage(), e);
}
}).map(fhirContext.newJsonParser().setSuppressNarratives(true)::parseResource).collect(Collectors.toList());

var bundleBuilder = new BundleBuilder(fhirContext);
resources.forEach(bundleBuilder::addTransactionCreateEntry);
return bundleBuilder.getBundle();

}

@NotNull
private IBaseBundle loadResourcesFromNPM() throws IOException {
if (Strings.isNullOrEmpty(packageId) && Strings.isNullOrEmpty(location)) {
LOG.error("No packageId or location supplied ... - exiting");
System.exit(-1);
}

packageManager = new FilesystemPackageCacheManager(true, new Random().nextInt());
packageManager = new FilesystemPackageCacheManager(FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);

if (!Strings.isNullOrEmpty(location)) {
installPackage();
}

final NpmPackage npmPackage = loadPackage();

final NpmPackage npmPackage = packageManager.loadPackage(packageId);
fhirContext = new FhirContext(FhirVersionEnum.forVersionString(npmPackage.fhirVersion()));

var clientFactory = fhirContext.getRestfulClientFactory();
clientFactory.setServerValidationMode(ServerValidationModeEnum.NEVER);

var bundleBuilder = new BundleBuilder(fhirContext);
loadResources(npmPackage).forEach(bundleBuilder::addTransactionCreateEntry);

if(!Strings.isNullOrEmpty(serverBase)) {
if (!Strings.isNullOrEmpty(seconds)) {
await().atMost(Integer.parseInt(seconds), TimeUnit.MINUTES).until(() -> serverReady(fhirContext, clientFactory));
}
}

emitBundle(bundleBuilder, fhirContext, clientFactory);
return loadResources(npmPackage);
}

private Boolean serverReady(FhirContext fhirContext, IRestfulClientFactory clientFactory) {
private Boolean serverReady(IRestfulClientFactory clientFactory) {

try {
clientFactory.newGenericClient(serverBase).search().forResource("StructureDefinition").execute();
Expand All @@ -130,8 +133,17 @@ private Boolean serverReady(FhirContext fhirContext, IRestfulClientFactory clien
}
}

private void emitBundle(BundleBuilder bundleBuilder, FhirContext fhirContext, IRestfulClientFactory clientFactory) {
var bundle = bundleBuilder.getBundle();
private void emitBundle(IBaseBundle bundle) {

var clientFactory = fhirContext.getRestfulClientFactory();
clientFactory.setServerValidationMode(ServerValidationModeEnum.NEVER);


if (!Strings.isNullOrEmpty(serverBase)) {
if (!Strings.isNullOrEmpty(seconds)) {
await().atMost(Integer.parseInt(seconds), TimeUnit.MINUTES).until(() -> serverReady(clientFactory));
}
}

if (Strings.isNullOrEmpty(serverBase)) {
LOG.info("Sending transaction bundle to console");
Expand All @@ -143,47 +155,18 @@ private void emitBundle(BundleBuilder bundleBuilder, FhirContext fhirContext, IR
}
}

private NpmPackage loadPackage() throws IOException {
try {
return packageManager.loadPackage(packageId);
} catch (NullPointerException npe) {
LOG.error("Could not load package: " + packageId);
LOG.info(npe.getMessage(), npe);
throw npe;
}
}

private void installPackage() throws IOException {
var npmAsBytes = loadPackageUrlContents(location);

var npmAsBytes = new PackageLoaderSvc().loadPackageUrlContents(location);
var npmPackage = NpmPackage.fromPackage(new ByteArrayInputStream(npmAsBytes));
packageManager.addPackageToCache(npmPackage.id(), npmPackage.version(), new ByteArrayInputStream(npmAsBytes), npmPackage.description());
LOG.warn("Overwriting parameterized packageId with packageId from location paramter. packageId was '" + packageId + "'. New packageId will be '" + npmPackage.id() + "#" + npmPackage.version() + "'");
packageId = npmPackage.id() + "#" + npmPackage.version();
}

private void loadFilesFromDirectory(String directory) {

var fhirContext = FhirContext.forR5();

List<IBaseResource> resources = Stream.of(new File(directory).listFiles()).filter(file -> !file.isDirectory()).filter(file -> file.getName().endsWith(".json")).filter(file -> file.getName().contains("mplementation")).map(f -> {
try {
return new String(Files.readAllBytes(Path.of(f.getPath())));
} catch (IOException e) {
throw new RuntimeException(e.getMessage(), e);
}
}).map(fhirContext.newJsonParser().setSuppressNarratives(true)::parseResource).collect(Collectors.toList());

var clientFactory = fhirContext.getRestfulClientFactory();
clientFactory.setServerValidationMode(ServerValidationModeEnum.NEVER);

var bundleBuilder = new BundleBuilder(fhirContext);
resources.forEach(bundleBuilder::addTransactionCreateEntry);
emitBundle(bundleBuilder, fhirContext, clientFactory);

}

@NotNull
private Collection<IBaseResource> loadResources(NpmPackage npmPackage) {
private IBaseBundle loadResources(NpmPackage npmPackage) {
Collection<IBaseResource> resources;
if (loadRecursively) {
resources = loadExampleResourcesRecursively(npmPackage);
Expand All @@ -194,7 +177,10 @@ private Collection<IBaseResource> loadResources(NpmPackage npmPackage) {
if (!includeSearchBundles) {
resources = resources.stream().filter(r -> !isSearchBundle.test(r)).collect(Collectors.toList());
}
return resources;

var bundleBuilder = new BundleBuilder(fhirContext);
resources.forEach(bundleBuilder::addTransactionCreateEntry);
return bundleBuilder.getBundle();
}

private @NotNull Collection<IBaseResource> loadExampleResourcesRecursively(NpmPackage npmPackage) {
Expand All @@ -211,7 +197,7 @@ private List<IBaseResource> loadExampleResources(NpmPackage npmPackage) {

if (exampleFolder == null) {
LOG.info("Found no example resources in " + npmPackage.name());
return Collections.EMPTY_LIST;
return List.of();
}

var fileNames = exampleFolder.getTypes().values().stream().flatMap(Collection::stream).collect(Collectors.toList());
Expand All @@ -226,8 +212,6 @@ private List<IBaseResource> loadExampleResources(NpmPackage npmPackage) {
}).map(fhirContext.newJsonParser().setSuppressNarratives(true)::parseResource).collect(Collectors.toList());
}

Function<String, FhirContext> toContext = (fhirVersionAsString) -> new FhirContext(FhirVersionEnum.forVersionString(fhirVersionAsString));

Function<String, NpmPackage> toNpmPackage = (nameAndVersion) -> {
try {
return packageManager.loadPackage(nameAndVersion);
Expand All @@ -237,50 +221,21 @@ private List<IBaseResource> loadExampleResources(NpmPackage npmPackage) {
};

Predicate<IBaseResource> isSearchBundle = (resource) -> {
if (org.hl7.fhir.dstu2.model.Bundle.class.isInstance(resource)) {
if (resource instanceof org.hl7.fhir.dstu2.model.Bundle) {
return ((org.hl7.fhir.dstu2.model.Bundle) resource).getTypeElement().getValue() == org.hl7.fhir.dstu2.model.Bundle.BundleType.SEARCHSET;
}
if (org.hl7.fhir.dstu3.model.Bundle.class.isInstance(resource)) {
if (resource instanceof org.hl7.fhir.dstu3.model.Bundle) {
return ((org.hl7.fhir.dstu3.model.Bundle) resource).getTypeElement().getValue() == org.hl7.fhir.dstu3.model.Bundle.BundleType.SEARCHSET;
}
if (org.hl7.fhir.r4.model.Bundle.class.isInstance(resource)) {
if (resource instanceof org.hl7.fhir.r4.model.Bundle) {
return ((org.hl7.fhir.r4.model.Bundle) resource).getTypeElement().getValue() == org.hl7.fhir.r4.model.Bundle.BundleType.SEARCHSET;
}
if (org.hl7.fhir.r4b.model.Bundle.class.isInstance(resource)) {
if (resource instanceof org.hl7.fhir.r4b.model.Bundle) {
return ((org.hl7.fhir.r4b.model.Bundle) resource).getTypeElement().getValue() == org.hl7.fhir.r4b.model.Bundle.BundleType.SEARCHSET;
}
if (org.hl7.fhir.r5.model.Bundle.class.isInstance(resource)) {
if (resource instanceof org.hl7.fhir.r5.model.Bundle) {
return ((org.hl7.fhir.r5.model.Bundle) resource).getTypeElement().getValue() == org.hl7.fhir.r5.model.Bundle.BundleType.SEARCHSET;
}
return false;
};

/**
* Copied and modified from ca.uhn.fhir.jpa.packages.JpaPackageCache in order to have some
* consistency
*
* @param thePackageUrl
* @return
*/
protected byte[] loadPackageUrlContents(String thePackageUrl) {
final byte[] bytes;
if (thePackageUrl.startsWith("file:")) {
try {
bytes = Files.readAllBytes(Paths.get(new URI(thePackageUrl)));
} catch (IOException | URISyntaxException e) {
throw new InternalErrorException(Msg.code(2024) + "Error loading \"" + thePackageUrl + "\": " + e.getMessage());
}
} else {
HttpClientConnectionManager connManager = new BasicHttpClientConnectionManager();
try (CloseableHttpResponse request = HttpClientBuilder.create().setConnectionManager(connManager).build().execute(new HttpGet(thePackageUrl))) {
if (request.getStatusLine().getStatusCode() != 200) {
throw new ResourceNotFoundException(Msg.code(1303) + "Received HTTP " + request.getStatusLine().getStatusCode() + " from URL: " + thePackageUrl);
}
bytes = IOUtils.toByteArray(request.getEntity().getContent());
} catch (IOException e) {
throw new InternalErrorException(Msg.code(1304) + "Error loading \"" + thePackageUrl + "\": " + e.getMessage());
}
}
return bytes;
}
}

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