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Code Issues Packages Projects Releases Wiki Activity

Don't install draft package contents (#2099) 

* Don't install draft package contents

* Add changelog

* Add changelog
This commit is contained in:
James Agnew 2020-09-22 09:44:36 -04:00 committed by GitHub
parent 072e63be5a
commit ef4f3df945
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9 changed files with 109 additions and 11 deletions
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6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2099_dont_install_draft_package_contents.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 2099
title: "When using an NPM package spec in STORE_AND_INSTALL mode, conformance resources will only be stored if they
have a status of `active`. This fixes a bug wgere installing the US Core IG caused searches to stop working due to
draft Search Parameters."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_2_0/2099_dont_override_sps_with_draft.yaml Normal file
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@ -0,0 +1,6 @@
---
type: add
issue: 2099
title: "Stored SearchParameter resources with a status of DRAFT will no longer override and disable existing built-in
search parameters. This is done in order to avoid issues caused by uploading NPM packages such as US Core that
contain a large number of draft parameters."

15
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/model/DaoMethodOutcome.java
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@ -28,6 +28,7 @@ public class DaoMethodOutcome extends MethodOutcome {
private IBasePersistedResource myEntity;
private IBaseResource myPreviousResource;
private boolean myNop;
/**
* Constructor
@ -36,6 +37,20 @@ public class DaoMethodOutcome extends MethodOutcome {
super();
}
/**
* Was this a NO-OP - Typically because of an update to a resource that already matched the contents provided
*/
public boolean isNop() {
return myNop;
}
/**
* Was this a NO-OP - Typically because of an update to a resource that already matched the contents provided
*/
public void setNop(boolean theNop) {
myNop = theNop;
}
public IBasePersistedResource getEntity() {
return myEntity;
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java
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@ -29,6 +29,7 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
@ -128,6 +129,12 @@ public abstract class BaseStorageDao {
protected DaoMethodOutcome toMethodOutcome(RequestDetails theRequest, @Nonnull final IBasePersistedResource theEntity, @Nonnull IBaseResource theResource) {
DaoMethodOutcome outcome = new DaoMethodOutcome();
if (theEntity instanceof ResourceTable) {
if (((ResourceTable) theEntity).isUnchangedInCurrentOperation()) {
outcome.setNop(true);
}
}
IIdType id = null;
if (theResource.getIdElement().getValue() != null) {
id = theResource.getIdElement();

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java
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@ -26,6 +26,7 @@ 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.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -35,7 +36,6 @@ 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.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.SearchParameterUtil;
import com.google.common.annotations.VisibleForTesting;
@ -208,6 +208,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
count[i] = resources.size();
for (IBaseResource next : resources) {
try {
next = isStructureDefinitionWithoutSnapshot(next) ? generateSnapshot(next) : next;
create(next, theOutcome);
@ -215,6 +216,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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);
}
}
}
@ -321,10 +323,11 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
} else {
ourLog.info("Updating existing resource matching {}", map.toNormalizedQueryString(myFhirContext));
theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
theResource.setId(searchResult.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless());
dao.update(theResource);
theResource.setId(searchResult.getResources(0, 1).get(0).getIdElement().toUnqualifiedVersionless());
DaoMethodOutcome outcome = dao.update(theResource);
if (!outcome.isNop()) {
theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
}
}
}
@ -349,6 +352,13 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
}
}
List<IPrimitiveType> statusTypes = myFhirContext.newFhirPath().evaluate(theResource, "status", IPrimitiveType.class);
if (statusTypes.size() > 0) {
if (!statusTypes.get(0).getValueAsString().equals("active")) {
return false;
}
}
return true;
}

19
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java
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@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
@ -462,6 +463,24 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
}
@Test
public void testBuiltInSearchParameterNotReplacedByDraftSearchParameter() {
myModelConfig.setDefaultSearchParamsCanBeOverridden(true);
SearchParameter memberSp = new SearchParameter();
memberSp.setCode("family");
memberSp.addBase("Patient");
memberSp.setType(Enumerations.SearchParamType.STRING);
memberSp.setExpression("Patient.name.family");
memberSp.setStatus(Enumerations.PublicationStatus.DRAFT);
mySearchParameterDao.create(memberSp, mySrd);
mySearchParamRegistry.forceRefresh();
RuntimeSearchParam sp = mySearchParamRegistry.getActiveSearchParam("Patient", "family");
assertEquals(RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE, sp.getStatus());
}
@Test

44
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmTestR4.java
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@ -49,6 +49,7 @@ import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@ -114,6 +115,20 @@ public class NpmTestR4 extends BaseJpaR4Test {
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.us.core").setVersion("3.1.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL).setFetchDependencies(true);
igInstaller.install(spec);
runInTransaction(()->{
SearchParameterMap map = SearchParameterMap.newSynchronous(SearchParameter.SP_BASE, new TokenParam("NamingSystem"));
IBundleProvider outcome = mySearchParameterDao.search(map);
List<IBaseResource> resources = outcome.getResources(0, outcome.sizeOrThrowNpe());
for (int i = 0; i < resources.size(); i++) {
ourLog.info("**************************************************************************");
ourLog.info("**************************************************************************");
ourLog.info("Res " + i);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resources.get(i)));
}
});
igInstaller.install(spec);
}
@ -162,7 +177,8 @@ public class NpmTestR4 extends BaseJpaR4Test {
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.12.0", bytes);
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.12.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
igInstaller.install(spec);
PackageInstallOutcomeJson outcome = igInstaller.install(spec);
assertEquals(1, outcome.getResourcesInstalled().get("CodeSystem"));
// Be sure no further communication with the server
JettyUtil.closeServer(myServer);
@ -215,11 +231,25 @@ public class NpmTestR4 extends BaseJpaR4Test {
runInTransaction(() -> {
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add(StructureDefinition.SP_URL, new UriParam("http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system"));
IBundleProvider outcome = myCodeSystemDao.search(map);
assertEquals(1, outcome.sizeOrThrowNpe());
IBundleProvider result = myCodeSystemDao.search(map);
assertEquals(1, result.sizeOrThrowNpe());
});
}
@Test
public void testInstallR4Package_DraftResourcesNotInstalled() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
byte[] bytes = loadClasspathBytes("/packages/test-draft-sample.tgz");
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.11.1", bytes);
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.11.1").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallOutcomeJson outcome = igInstaller.install(spec);
assertEquals(0, outcome.getResourcesInstalled().size(), outcome.getResourcesInstalled().toString());
}
@Test
public void testInstallR4Package_Twice() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
@ -236,6 +266,11 @@ public class NpmTestR4 extends BaseJpaR4Test {
igInstaller.install(spec);
outcome = igInstaller.install(spec);
assertEquals(null, outcome.getResourcesInstalled().get("CodeSystem"));
// Ensure that we loaded the contents
IBundleProvider searchResult = myCodeSystemDao.search(SearchParameterMap.newSynchronous("url", new UriParam("http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system")));
assertEquals(1, searchResult.sizeOrThrowNpe());
}
@ -257,9 +292,6 @@ public class NpmTestR4 extends BaseJpaR4Test {
assertEquals(null, pkg.description());
assertEquals("UK.Core.r4", pkg.name());
// Ensure that we loaded the contents
IBundleProvider searchResult = myStructureDefinitionDao.search(SearchParameterMap.newSynchronous("url", new UriParam("https://fhir.nhs.uk/R4/StructureDefinition/UKCore-Patient")));
assertEquals(1, searchResult.sizeOrThrowNpe());
}
@Test

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hapi-fhir-jpaserver-base/src/test/resources/packages/test-draft-sample.tgz Normal file
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3
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/SearchParamRegistryImpl.java
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@ -291,6 +291,9 @@ public class SearchParamRegistryImpl implements ISearchParamRegistry {
if (runtimeSp == null) {
continue;
}
if (runtimeSp.getStatus() == RuntimeSearchParam.RuntimeSearchParamStatusEnum.DRAFT) {
continue;
}
for (String nextBaseName : SearchParameterUtil.getBaseAsStrings(myFhirContext, nextSp)) {
if (isBlank(nextBaseName)) {