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Cleanup of package installer

This commit is contained in:
jamesagnew 2020-07-21 11:43:57 -04:00
parent c44c1ff11f
commit 5f1078ac13
5 changed files with 101 additions and 88 deletions
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20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallOutcomeJson.java
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@ -26,7 +26,9 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import io.swagger.annotations.ApiModel;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@ApiModel("Represents an NPM package installation response")
@JsonInclude(JsonInclude.Include.NON_NULL)
@ -36,6 +38,9 @@ public class PackageInstallOutcomeJson {
@JsonProperty("messages")
private List<String> myMessage;
@JsonProperty("resourcesInstalled")
private Map<String, Integer> myResourcesInstalled;
public List<String> getMessage() {
if (myMessage == null) {
myMessage = new ArrayList<>();
@ -43,4 +48,19 @@ public class PackageInstallOutcomeJson {
return myMessage;
}
public Map<String, Integer> getResourcesInstalled() {
if (myResourcesInstalled == null) {
myResourcesInstalled = new HashMap<>();
}
return myResourcesInstalled;
}
public void incrementResourcesInstalled(String theResourceType) {
Integer existing = getResourcesInstalled().get(theResourceType);
if (existing == null) {
getResourcesInstalled().put(theResourceType, 1);
} else {
getResourcesInstalled().put(theResourceType, existing + 1);
}
}
}

132
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java
View File

@ -26,12 +26,13 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.SearchParameterUtil;
@ -48,6 +49,8 @@ import org.hl7.fhir.utilities.cache.NpmPackage;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
import java.io.IOException;
@ -57,6 +60,7 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -85,7 +89,11 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
@Autowired
private IValidationSupport validationSupport;
@Autowired
private IHapiPackageCacheManager packageCacheManager;
private IHapiPackageCacheManager myPackageCacheManager;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private INpmPackageVersionDao myPackageVersionDao;
/**
* Constructor
@ -125,12 +133,22 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
*
* @param theInstallationSpec The details about what should be installed
*/
@SuppressWarnings("ConstantConditions")
@Override
public PackageInstallOutcomeJson install(PackageInstallationSpec theInstallationSpec) throws ImplementationGuideInstallationException {
PackageInstallOutcomeJson retVal = new PackageInstallOutcomeJson();
if (enabled) {
try {
NpmPackage npmPackage = packageCacheManager.installPackage(theInstallationSpec);
boolean exists = new TransactionTemplate(myTxManager).execute(tx -> {
Optional<NpmPackageVersionEntity> existing = myPackageVersionDao.findByPackageIdAndVersion(theInstallationSpec.getName(), theInstallationSpec.getVersion());
return existing.isPresent();
});
if (exists) {
ourLog.info("Package {}#{} is already installed", theInstallationSpec.getName(), theInstallationSpec.getVersion());
}
NpmPackage npmPackage = myPackageCacheManager.installPackage(theInstallationSpec);
if (npmPackage == null) {
throw new IOException("Package not found");
}
@ -142,7 +160,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
}
if (theInstallationSpec.getInstallMode() == PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL) {
install(npmPackage, theInstallationSpec);
install(npmPackage, theInstallationSpec, retVal);
}
} catch (IOException e) {
@ -160,7 +178,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
*
* @throws ImplementationGuideInstallationException if installation fails
*/
private void install(NpmPackage npmPackage, PackageInstallationSpec theInstallationSpec) throws ImplementationGuideInstallationException {
private void install(NpmPackage npmPackage, PackageInstallationSpec theInstallationSpec, PackageInstallOutcomeJson theOutcome) throws ImplementationGuideInstallationException {
String name = npmPackage.getNpm().get("name").getAsString();
String version = npmPackage.getNpm().get("version").getAsString();
@ -182,13 +200,16 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
Collection<IBaseResource> resources = parseResourcesOfType(installTypes.get(i), npmPackage);
count[i] = resources.size();
try {
resources.stream()
.map(r -> isStructureDefinitionWithoutSnapshot(r) ? generateSnapshot(r) : r)
.forEach(r -> createOrUpdate(r));
} catch (Exception e) {
throw new ImplementationGuideInstallationException(String.format("Error installing IG %s#%s: %s", name, version, e.toString()), e);
for (IBaseResource next : resources) {
try {
next = isStructureDefinitionWithoutSnapshot(next) ? generateSnapshot(next) : next;
create(next, theOutcome);
} catch (Exception e) {
ourLog.warn("Failed to upload resource of type {} with ID {} - Error: {}", myFhirContext.getResourceType(next), next.getIdElement().getValue(), e.toString());
throw new ImplementationGuideInstallationException(String.format("Error installing IG %s#%s: %s", name, version, e.toString()), e);
}
}
}
ourLog.info(String.format("Finished installation of package %s#%s:", name, version));
@ -220,13 +241,13 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
}
// resolve in local cache or on packages.fhir.org
NpmPackage dependency = packageCacheManager.loadPackage(id, ver);
NpmPackage dependency = myPackageCacheManager.loadPackage(id, ver);
// recursive call to install dependencies of a package before
// installing the package
fetchAndInstallDependencies(dependency, theInstallationSpec, theOutcome);
if (theInstallationSpec.getInstallMode() == PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL) {
install(dependency, theInstallationSpec);
install(dependency, theInstallationSpec, theOutcome);
}
} catch (IOException e) {
@ -260,9 +281,9 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
* ============================= Utility methods ===============================
*/
private Collection<IBaseResource> parseResourcesOfType(String type, NpmPackage pkg) {
private List<IBaseResource> parseResourcesOfType(String type, NpmPackage pkg) {
if (!pkg.getFolders().containsKey("package")) {
return Collections.EMPTY_LIST;
return Collections.emptyList();
}
ArrayList<IBaseResource> resources = new ArrayList<>();
List<String> filesForType = pkg.getFolders().get("package").getTypes().get(type);
@ -279,28 +300,17 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
return resources;
}
/**
* Create a resource or update it, if its already existing.
*/
private void createOrUpdate(IBaseResource resource) {
try {
IFhirResourceDao dao = myDaoRegistry.getResourceDao(resource.getClass());
IBundleProvider searchResult = dao.search(createSearchParameterMapFor(resource));
if (searchResult.isEmpty()) {
private void create(IBaseResource theResource, PackageInstallOutcomeJson theOutcome) {
IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
SearchParameterMap map = createSearchParameterMapFor(theResource);
IBundleProvider searchResult = dao.search(map);
if (searchResult.isEmpty()) {
if (validForUpload(resource)) {
dao.create(resource);
}
} else {
IBaseResource existingResource = verifySearchResultFor(resource, searchResult);
if (existingResource != null) {
resource.setId(existingResource.getIdElement().getValue());
dao.update(resource);
}
if (validForUpload(theResource)) {
theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
dao.create(theResource);
}
} catch (BaseServerResponseException e) {
ourLog.warn("Failed to upload resource of type {} with ID {} - Error: {}", myFhirContext.getResourceType(resource), resource.getIdElement().getValue(), e.toString());
}
}
@ -344,40 +354,13 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
private SearchParameterMap createSearchParameterMapFor(IBaseResource resource) {
if (resource.getClass().getSimpleName().equals("NamingSystem")) {
String uniqueId = extractUniqeIdFromNamingSystem(resource);
return new SearchParameterMap().add("value", new StringParam(uniqueId).setExact(true));
return SearchParameterMap.newSynchronous().add("value", new StringParam(uniqueId).setExact(true));
} else if (resource.getClass().getSimpleName().equals("Subscription")) {
String id = extractIdFromSubscription(resource);
return new SearchParameterMap().add("_id", new TokenParam(id));
return SearchParameterMap.newSynchronous().add("_id", new TokenParam(id));
} else {
String url = extractUniqueUrlFromMetadataResouce(resource);
return new SearchParameterMap().add("url", new UriParam(url));
}
}
private IBaseResource verifySearchResultFor(IBaseResource resource, IBundleProvider searchResult) {
FhirTerser terser = myFhirContext.newTerser();
if (resource.getClass().getSimpleName().equals("NamingSystem")) {
if (searchResult.size() > 1) {
ourLog.warn("Expected 1 NamingSystem with unique ID {}, found {}. Will not attempt to update resource.",
extractUniqeIdFromNamingSystem(resource), searchResult.size());
return null;
}
return getFirstResourceFrom(searchResult);
} else if (resource.getClass().getSimpleName().equals("Subscription")) {
if (searchResult.size() > 1) {
ourLog.warn("Expected 1 Subscription with ID {}, found {}. Will not attempt to update resource.",
extractIdFromSubscription(resource), searchResult.size());
return null;
}
return getFirstResourceFrom(searchResult);
} else {
// Resource is of type CodeSystem, ValueSet, StructureDefinition, ConceptMap or SearchParameter
if (searchResult.size() > 1) {
ourLog.warn("Expected 1 MetadataResource with globally unique URL {}, found {}. " +
"Will not attempt to update resource.", extractUniqueUrlFromMetadataResouce(resource), searchResult.size());
return null;
}
return getFirstResourceFrom(searchResult);
String url = extractUniqueUrlFromMetadataResource(resource);
return SearchParameterMap.newSynchronous().add("url", new UriParam(url));
}
}
@ -387,19 +370,19 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
if (uniqueIdComponent == null) {
throw new ImplementationGuideInstallationException("NamingSystem does not have uniqueId component.");
}
IPrimitiveType asPrimitiveType = (IPrimitiveType) terser.getSingleValueOrNull(uniqueIdComponent, "value");
IPrimitiveType<?> asPrimitiveType = (IPrimitiveType<?>) terser.getSingleValueOrNull(uniqueIdComponent, "value");
return (String) asPrimitiveType.getValue();
}
private String extractIdFromSubscription(IBaseResource resource) {
FhirTerser terser = myFhirContext.newTerser();
IPrimitiveType asPrimitiveType = (IPrimitiveType) terser.getSingleValueOrNull(resource, "id");
IPrimitiveType<?> asPrimitiveType = (IPrimitiveType<?>) terser.getSingleValueOrNull(resource, "id");
return (String) asPrimitiveType.getValue();
}
private String extractUniqueUrlFromMetadataResouce(IBaseResource resource) {
private String extractUniqueUrlFromMetadataResource(IBaseResource resource) {
FhirTerser terser = myFhirContext.newTerser();
IPrimitiveType asPrimitiveType = (IPrimitiveType) terser.getSingleValueOrNull(resource, "url");
IPrimitiveType<?> asPrimitiveType = (IPrimitiveType<?>) terser.getSingleValueOrNull(resource, "url");
return (String) asPrimitiveType.getValue();
}
@ -408,13 +391,4 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
myFhirContext = theCtx;
}
private static IBaseResource getFirstResourceFrom(IBundleProvider searchResult) {
try {
return searchResult.getResources(0, 0).get(0);
} catch (IndexOutOfBoundsException e) {
ourLog.warn("Error when extracting resource from search result " +
"(search result should have been non-empty))", e);
return null;
}
}
}

19
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmTestR4.java
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@ -211,6 +211,25 @@ public class NpmTestR4 extends BaseJpaR4Test {
});
}
@Test
public void testInstallR4Package_Twice() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
byte[] bytes = loadClasspathBytes("/packages/hl7.fhir.uv.shorthand-0.12.0.tgz");
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.12.0", bytes);
PackageInstallOutcomeJson outcome;
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.12.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
outcome = igInstaller.install(spec);
assertEquals(1, outcome.getResourcesInstalled().get("CodeSystem"));
igInstaller.install(spec);
outcome = igInstaller.install(spec);
assertEquals(null, outcome.getResourcesInstalled().get("CodeSystem"));
}
@Test
public void testInstallR4PackageWithNoDescription() throws Exception {

6
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/ExtendedPatientTest.java
View File

@ -6,10 +6,10 @@ import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertSame;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertSame;
public class ExtendedPatientTest {

12
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/ExtendedPatientTest.java
View File

@ -1,15 +1,15 @@
package ca.uhn.fhir.parser;
import ca.uhn.fhir.context.FhirContext;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertSame;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertSame;
public class ExtendedPatientTest {
@ -45,8 +45,8 @@ public class ExtendedPatientTest {
Bundle parsedBundle = p.parseResource(Bundle.class, encoded);
ExtendedPatient parsedHomer = (ExtendedPatient)parsedBundle.getEntry().get(0).getResource();
ExtendedPatient parsedMarge = (ExtendedPatient)parsedBundle.getEntry().get(1).getResource();
ExtendedPatient parsedHomer = (ExtendedPatient) parsedBundle.getEntry().get(0).getResource();
ExtendedPatient parsedMarge = (ExtendedPatient) parsedBundle.getEntry().get(1).getResource();
IBaseResource referencedHomer = parsedMarge.getLinkFirstRep().getOther().getResource();
assertNotNull(referencedHomer);