use SearchParamater validator in package installer (#6112)
This commit is contained in:
Emre Dincturk
GitHub
parent
39cbec8aa4
commit
13e2d41165
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@ -0,0 +1,6 @@
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---
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type: fix
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issue: 6111
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title: "Previously, the package installer wouldn't create a composite SearchParameter resource if the SearchParameter
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resource didn't have an expression element at the root level. This has now been fixed by making
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SearchParameter validation in package installer consistent with the DAO level validations."
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@ -34,6 +34,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
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import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
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import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
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import ca.uhn.fhir.jpa.dao.validation.SearchParameterDaoValidator;
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import ca.uhn.fhir.jpa.model.config.PartitionSettings;
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import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
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import ca.uhn.fhir.jpa.packages.loader.PackageResourceParsingSvc;
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@ -47,8 +48,10 @@ import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.param.UriParam;
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import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.FhirTerser;
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import ca.uhn.fhir.util.SearchParameterUtil;
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import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
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import com.google.common.annotations.VisibleForTesting;
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import jakarta.annotation.PostConstruct;
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import org.apache.commons.lang3.Validate;
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@ -73,7 +76,6 @@ import java.util.Optional;
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import static ca.uhn.fhir.jpa.packages.util.PackageUtils.DEFAULT_INSTALL_TYPES;
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import static ca.uhn.fhir.util.SearchParameterUtil.getBaseAsStrings;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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/**
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* @since 5.1.0
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@ -117,6 +119,12 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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@Autowired
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private JpaStorageSettings myStorageSettings;
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@Autowired
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private SearchParameterDaoValidator mySearchParameterDaoValidator;
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@Autowired
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private VersionCanonicalizer myVersionCanonicalizer;
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/**
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* Constructor
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*/
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@ -431,6 +439,23 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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return outcome != null && !outcome.isNop();
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}
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/*
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* This function helps preserve the resource types in the base of an existing SP when an overriding SP's base
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* covers only a subset of the existing base.
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*
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* For example, say for an existing SP,
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* - the current base is: [ResourceTypeA, ResourceTypeB]
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* - the new base is: [ResourceTypeB]
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*
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* If we were to overwrite the existing SP's base to the new base ([ResourceTypeB]) then the
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* SP would stop working on ResourceTypeA, which would be a loss of functionality.
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*
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* Instead, this function updates the existing SP's base by removing the resource types that
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* are covered by the overriding SP.
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* In our example, this function updates the existing SP's base to [ResourceTypeA], so that the existing SP
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* still works on ResourceTypeA, and the caller then creates a new SP that covers ResourceTypeB.
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* https://github.com/hapifhir/hapi-fhir/issues/5366
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*/
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private boolean updateExistingResourceIfNecessary(
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IFhirResourceDao theDao, IBaseResource theResource, IBaseResource theExistingResource) {
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if (!"SearchParameter".equals(theResource.getClass().getSimpleName())) {
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@ -506,33 +531,9 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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boolean validForUpload(IBaseResource theResource) {
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String resourceType = myFhirContext.getResourceType(theResource);
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if ("SearchParameter".equals(resourceType)) {
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String code = SearchParameterUtil.getCode(myFhirContext, theResource);
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if (!isBlank(code) && code.startsWith("_")) {
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ourLog.warn(
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"Failed to validate resource of type {} with url {} - Error: Resource code starts with \"_\"",
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theResource.fhirType(),
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SearchParameterUtil.getURL(myFhirContext, theResource));
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return false;
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}
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String expression = SearchParameterUtil.getExpression(myFhirContext, theResource);
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if (isBlank(expression)) {
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ourLog.warn(
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"Failed to validate resource of type {} with url {} - Error: Resource expression is blank",
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theResource.fhirType(),
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SearchParameterUtil.getURL(myFhirContext, theResource));
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return false;
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}
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if (getBaseAsStrings(myFhirContext, theResource).isEmpty()) {
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ourLog.warn(
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"Failed to validate resource of type {} with url {} - Error: Resource base is empty",
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theResource.fhirType(),
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SearchParameterUtil.getURL(myFhirContext, theResource));
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return false;
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}
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if ("SearchParameter".equals(resourceType) && !isValidSearchParameter(theResource)) {
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// this is an invalid search parameter
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return false;
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}
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if (!isValidResourceStatusForPackageUpload(theResource)) {
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@ -546,6 +547,21 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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return true;
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}
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private boolean isValidSearchParameter(IBaseResource theResource) {
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try {
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org.hl7.fhir.r5.model.SearchParameter searchParameter =
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myVersionCanonicalizer.searchParameterToCanonical(theResource);
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mySearchParameterDaoValidator.validate(searchParameter);
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return true;
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} catch (UnprocessableEntityException unprocessableEntityException) {
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ourLog.error(
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"The SearchParameter with URL {} is invalid. Validation Error: {}",
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SearchParameterUtil.getURL(myFhirContext, theResource),
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unprocessableEntityException.getMessage());
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return false;
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}
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}
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/**
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* For resources like {@link org.hl7.fhir.r4.model.Subscription}, {@link org.hl7.fhir.r4.model.DocumentReference},
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* and {@link org.hl7.fhir.r4.model.Communication}, the status field doesn't necessarily need to be set to 'active'
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@ -569,9 +585,13 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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List<IPrimitiveType> statusTypes =
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myFhirContext.newFhirPath().evaluate(theResource, "status", IPrimitiveType.class);
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// Resource does not have a status field
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if (statusTypes.isEmpty()) return true;
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if (statusTypes.isEmpty()) {
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return true;
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}
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// Resource has a null status field
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if (statusTypes.get(0).getValue() == null) return false;
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if (statusTypes.get(0).getValue() == null) {
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return false;
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}
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// Resource has a status, and we need to check based on type
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switch (theResource.fhirType()) {
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case "Subscription":
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@ -9,13 +9,20 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
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import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
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import ca.uhn.fhir.jpa.dao.tx.NonTransactionalHapiTransactionService;
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import ca.uhn.fhir.jpa.dao.validation.SearchParameterDaoValidator;
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import ca.uhn.fhir.jpa.model.config.PartitionSettings;
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import ca.uhn.fhir.jpa.packages.loader.PackageResourceParsingSvc;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistryController;
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import ca.uhn.fhir.jpa.searchparam.util.SearchParameterHelper;
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import ca.uhn.fhir.mdm.log.Logs;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.server.SimpleBundleProvider;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.hapi.converters.canonical.VersionCanonicalizer;
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import ca.uhn.test.util.LogbackTestExtension;
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import ca.uhn.test.util.LogbackTestExtensionAssert;
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import ch.qos.logback.classic.Logger;
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import jakarta.annotation.Nonnull;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.CodeSystem;
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@ -24,6 +31,7 @@ import org.hl7.fhir.r4.model.Communication;
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import org.hl7.fhir.r4.model.DocumentReference;
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import org.hl7.fhir.r4.model.Enumerations;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.SearchParameter;
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import org.hl7.fhir.r4.model.Subscription;
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import org.hl7.fhir.utilities.npm.NpmPackage;
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@ -31,6 +39,7 @@ import org.hl7.fhir.utilities.npm.PackageGenerator;
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import org.junit.jupiter.api.Nested;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.junit.jupiter.api.extension.RegisterExtension;
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import org.junit.jupiter.params.ParameterizedTest;
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import org.junit.jupiter.params.provider.Arguments;
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import org.junit.jupiter.params.provider.MethodSource;
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@ -40,6 +49,7 @@ import org.mockito.InjectMocks;
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import org.mockito.Mock;
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import org.mockito.Spy;
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import org.mockito.junit.jupiter.MockitoExtension;
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import org.slf4j.LoggerFactory;
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import java.io.ByteArrayOutputStream;
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import java.io.IOException;
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@ -52,8 +62,14 @@ import java.util.Optional;
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import java.util.stream.Stream;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import static org.junit.jupiter.api.Assertions.assertThrows;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.params.provider.Arguments.arguments;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.Mockito.doNothing;
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import static org.mockito.Mockito.doReturn;
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import static org.mockito.Mockito.doThrow;
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import static org.mockito.Mockito.times;
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import static org.mockito.Mockito.verify;
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import static org.mockito.Mockito.when;
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@ -63,6 +79,10 @@ public class PackageInstallerSvcImplTest {
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public static final String PACKAGE_VERSION = "1.0";
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public static final String PACKAGE_ID_1 = "package1";
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@RegisterExtension
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LogbackTestExtension myLogCapture = new LogbackTestExtension(LoggerFactory.getLogger(PackageInstallerSvcImpl.class));
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@Mock
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private INpmPackageVersionDao myPackageVersionDao;
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@Mock
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@ -83,6 +103,13 @@ public class PackageInstallerSvcImplTest {
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private SearchParameterMap mySearchParameterMap;
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@Mock
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private JpaStorageSettings myStorageSettings;
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@Mock
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private VersionCanonicalizer myVersionCanonicalizerMock;
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@Mock
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private SearchParameterDaoValidator mySearchParameterDaoValidatorMock;
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@Spy
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private FhirContext myCtx = FhirContext.forR4Cached();
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@Spy
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@ -91,6 +118,8 @@ public class PackageInstallerSvcImplTest {
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private PackageResourceParsingSvc myPackageResourceParsingSvc = new PackageResourceParsingSvc(myCtx);
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@Spy
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private PartitionSettings myPartitionSettings = new PartitionSettings();
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@InjectMocks
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private PackageInstallerSvcImpl mySvc;
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@ -110,66 +139,97 @@ public class PackageInstallerSvcImplTest {
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@Nested
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class ValidForUploadTest {
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public static Stream<Arguments> parametersIsValidForUpload() {
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SearchParameter sp1 = new SearchParameter();
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sp1.setCode("_id");
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// Patient resource doesn't have a status element in FHIR spec
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Patient resourceWithNoStatusElementInSpec = new Patient();
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SearchParameter sp2 = new SearchParameter();
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sp2.setCode("name");
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sp2.setExpression("Patient.name");
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sp2.setStatus(Enumerations.PublicationStatus.ACTIVE);
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SearchParameter spWithActiveStatus = new SearchParameter();
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spWithActiveStatus.setStatus(Enumerations.PublicationStatus.ACTIVE);
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SearchParameter sp3 = new SearchParameter();
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sp3.setCode("name");
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sp3.addBase("Patient");
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sp3.setStatus(Enumerations.PublicationStatus.ACTIVE);
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SearchParameter spWithDraftStatus = new SearchParameter();
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spWithDraftStatus.setStatus(Enumerations.PublicationStatus.DRAFT);
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SearchParameter sp4 = new SearchParameter();
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sp4.setCode("name");
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sp4.addBase("Patient");
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sp4.setExpression("Patient.name");
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sp4.setStatus(Enumerations.PublicationStatus.ACTIVE);
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SearchParameter sp5 = new SearchParameter();
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sp5.setCode("name");
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sp5.addBase("Patient");
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sp5.setExpression("Patient.name");
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sp5.setStatus(Enumerations.PublicationStatus.DRAFT);
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SearchParameter spWithNullStatus = new SearchParameter();
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spWithNullStatus.setStatus(null);
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return Stream.of(
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arguments(sp1, false, false),
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arguments(sp2, false, true),
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arguments(sp3, false, true),
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arguments(sp4, true, true),
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arguments(sp5, true, false),
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arguments(createSubscription(Subscription.SubscriptionStatus.REQUESTED), true, true),
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arguments(createSubscription(Subscription.SubscriptionStatus.ERROR), true, false),
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arguments(createSubscription(Subscription.SubscriptionStatus.ACTIVE), true, false),
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arguments(createDocumentReference(Enumerations.DocumentReferenceStatus.ENTEREDINERROR), true, true),
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arguments(createDocumentReference(Enumerations.DocumentReferenceStatus.NULL), true, false),
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arguments(createDocumentReference(null), true, false),
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arguments(createCommunication(Communication.CommunicationStatus.NOTDONE), true, true),
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arguments(createCommunication(Communication.CommunicationStatus.NULL), true, false),
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arguments(createCommunication(null), true, false));
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arguments(resourceWithNoStatusElementInSpec, true),
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arguments(spWithActiveStatus, true),
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arguments(spWithNullStatus, false),
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arguments(spWithDraftStatus, false),
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arguments(createSubscription(Subscription.SubscriptionStatus.REQUESTED), true),
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arguments(createSubscription(Subscription.SubscriptionStatus.ERROR), false),
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arguments(createSubscription(Subscription.SubscriptionStatus.ACTIVE), false),
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arguments(createDocumentReference(Enumerations.DocumentReferenceStatus.ENTEREDINERROR), true),
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arguments(createDocumentReference(Enumerations.DocumentReferenceStatus.NULL), false),
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arguments(createDocumentReference(null), false),
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arguments(createCommunication(Communication.CommunicationStatus.NOTDONE), true),
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arguments(createCommunication(Communication.CommunicationStatus.NULL), false),
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arguments(createCommunication(null), false));
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}
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@ParameterizedTest
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@MethodSource(value = "parametersIsValidForUpload")
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public void testValidForUpload_withResource(IBaseResource theResource,
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boolean theTheMeetsOtherFilterCriteria,
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boolean theMeetsStatusFilterCriteria) {
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if (theTheMeetsOtherFilterCriteria) {
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when(myStorageSettings.isValidateResourceStatusForPackageUpload()).thenReturn(true);
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public void testValidForUpload_WhenStatusValidationSettingIsEnabled_ValidatesResourceStatus(IBaseResource theResource,
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boolean theExpectedResultForStatusValidation) {
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if (theResource.fhirType().equals("SearchParameter")) {
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setupSearchParameterValidationMocksForSuccess();
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}
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assertEquals(theTheMeetsOtherFilterCriteria && theMeetsStatusFilterCriteria, mySvc.validForUpload(theResource));
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when(myStorageSettings.isValidateResourceStatusForPackageUpload()).thenReturn(true);
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assertEquals(theExpectedResultForStatusValidation, mySvc.validForUpload(theResource));
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}
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if (theTheMeetsOtherFilterCriteria) {
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when(myStorageSettings.isValidateResourceStatusForPackageUpload()).thenReturn(false);
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@ParameterizedTest
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@MethodSource(value = "parametersIsValidForUpload")
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public void testValidForUpload_WhenStatusValidationSettingIsDisabled_DoesNotValidateResourceStatus(IBaseResource theResource) {
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if (theResource.fhirType().equals("SearchParameter")) {
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setupSearchParameterValidationMocksForSuccess();
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}
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assertEquals(theTheMeetsOtherFilterCriteria, mySvc.validForUpload(theResource));
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when(myStorageSettings.isValidateResourceStatusForPackageUpload()).thenReturn(false);
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//all resources should pass status validation in this case, so expect true always
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assertTrue(mySvc.validForUpload(theResource));
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}
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@Test
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public void testValidForUpload_WhenSearchParameterIsInvalid_ReturnsFalse() {
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final String validationExceptionMessage = "This SP is invalid!!";
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final String spURL = "http://myspurl.example/invalidsp";
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SearchParameter spR4 = new SearchParameter();
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spR4.setUrl(spURL);
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org.hl7.fhir.r5.model.SearchParameter spR5 = new org.hl7.fhir.r5.model.SearchParameter();
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when(myVersionCanonicalizerMock.searchParameterToCanonical(spR4)).thenReturn(spR5);
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doThrow(new UnprocessableEntityException(validationExceptionMessage)).
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when(mySearchParameterDaoValidatorMock).validate(spR5);
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assertFalse(mySvc.validForUpload(spR4));
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final String expectedLogMessage = String.format(
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"The SearchParameter with URL %s is invalid. Validation Error: %s", spURL, validationExceptionMessage);
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LogbackTestExtensionAssert.assertThat(myLogCapture).hasErrorMessage(expectedLogMessage);
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}
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@Test
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public void testValidForUpload_WhenSearchParameterValidatorThrowsAnExceptionOtherThanUnprocessableEntityException_ThenThrows() {
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SearchParameter spR4 = new SearchParameter();
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org.hl7.fhir.r5.model.SearchParameter spR5 = new org.hl7.fhir.r5.model.SearchParameter();
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RuntimeException notAnUnprocessableEntityException = new RuntimeException("should not be caught");
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when(myVersionCanonicalizerMock.searchParameterToCanonical(spR4)).thenReturn(spR5);
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doThrow(notAnUnprocessableEntityException).
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when(mySearchParameterDaoValidatorMock).validate(spR5);
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Exception actualExceptionThrown = assertThrows(Exception.class, () -> mySvc.validForUpload(spR4));
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assertEquals(notAnUnprocessableEntityException, actualExceptionThrown);
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}
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}
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@Test
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public void testDontTryToInstallDuplicateCodeSystem_CodeSystemAlreadyExistsWithDifferentId() throws IOException {
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// Setup
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@ -296,6 +356,11 @@ public class PackageInstallerSvcImplTest {
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return pkg;
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}
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private void setupSearchParameterValidationMocksForSuccess() {
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when(myVersionCanonicalizerMock.searchParameterToCanonical(any())).thenReturn(new org.hl7.fhir.r5.model.SearchParameter());
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doNothing().when(mySearchParameterDaoValidatorMock).validate(any());
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}
|
||||
|
||||
private static SearchParameter createSearchParameter(String theId, Collection<String> theBase) {
|
||||
SearchParameter searchParameter = new SearchParameter();
|
||||
if (theId != null) {
|
||||
|
|
@ -330,4 +395,5 @@ public class PackageInstallerSvcImplTest {
|
|||
communication.setStatus(theCommunicationStatus);
|
||||
return communication;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -360,7 +360,22 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testCreateInvalidParamNoPath() {
|
||||
public void testCreateCompositeParamNoExpressionAtRootLevel() {
|
||||
// allow composite search parameter to have no expression element at root level on the resource
|
||||
SearchParameter fooSp = new SearchParameter();
|
||||
fooSp.addBase("Patient");
|
||||
fooSp.setCode("foo");
|
||||
fooSp.setType(Enumerations.SearchParamType.COMPOSITE);
|
||||
fooSp.setTitle("FOO SP");
|
||||
fooSp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE);
|
||||
|
||||
// Ensure that no exceptions are thrown
|
||||
mySearchParameterDao.create(fooSp, mySrd);
|
||||
mySearchParamRegistry.forceRefresh();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreateInvalidParamNoExpression() {
|
||||
SearchParameter fooSp = new SearchParameter();
|
||||
fooSp.addBase("Patient");
|
||||
fooSp.setCode("foo");
|
||||
|
|
|
|||
|
|
@ -9,10 +9,16 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
|
|||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
|
||||
import ca.uhn.fhir.model.primitive.IdDt;
|
||||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.rest.param.TokenParam;
|
||||
import com.github.dnault.xmlpatch.repackaged.org.jaxen.util.SingletonList;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.hl7.fhir.r4.model.CodeType;
|
||||
import org.hl7.fhir.r4.model.Enumerations;
|
||||
import org.hl7.fhir.r4.model.NamingSystem;
|
||||
import org.hl7.fhir.r4.model.SearchParameter;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.hl7.fhir.utilities.npm.NpmPackage;
|
||||
import org.hl7.fhir.utilities.npm.PackageGenerator;
|
||||
|
|
@ -149,6 +155,24 @@ public class PackageInstallerSvcImplCreateTest extends BaseJpaR4Test {
|
|||
assertEquals(copyright2, actualValueSet2.getCopyright());
|
||||
}
|
||||
|
||||
@Test
|
||||
void installCompositeSearchParameterWithNoExpressionAtRoot() throws IOException {
|
||||
final String spCode = "my-test-composite-sp-with-no-expression";
|
||||
SearchParameter spR4 = new SearchParameter();
|
||||
spR4.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
spR4.setType(Enumerations.SearchParamType.COMPOSITE);
|
||||
spR4.setBase(List.of(new CodeType("Patient")));
|
||||
spR4.setCode(spCode);
|
||||
|
||||
install(spR4);
|
||||
|
||||
// verify the SP is created
|
||||
SearchParameterMap map = SearchParameterMap.newSynchronous()
|
||||
.add(SearchParameter.SP_CODE, new TokenParam(spCode));
|
||||
IBundleProvider outcome = mySearchParameterDao.search(map);
|
||||
assertEquals(1, outcome.size());
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
private List<ValueSet> getAllValueSets() {
|
||||
final List<IBaseResource> allResources = myValueSetDao.search(SearchParameterMap.newSynchronous(), REQUEST_DETAILS).getAllResources();
|
||||
|
|
|
|||
Loading…
Reference in New Issue