Address issues when importing US Core (#1986)
* Work on US Core import * Work on US Core * Resolve issues with US Core import * Test fix
This commit is contained in:
James Agnew
GitHub
parent
c13e17b4e6
commit
5db90d3e6e
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@ -28,6 +28,7 @@ import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import javax.annotation.Nullable;
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import java.util.ArrayList;
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import java.util.List;
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@ -49,4 +50,27 @@ public class SearchParameterUtil {
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return retVal;
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}
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@Nullable
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public static String getCode(FhirContext theContext, IBaseResource theResource) {
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return getStringChild(theContext, theResource, "code");
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}
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@Nullable
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public static String getExpression(FhirContext theFhirContext, IBaseResource theResource) {
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return getStringChild(theFhirContext, theResource, "expression");
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}
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private static String getStringChild(FhirContext theFhirContext, IBaseResource theResource, String theChildName) {
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Validate.notNull(theFhirContext, "theContext must not be null");
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Validate.notNull(theResource, "theResource must not be null");
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RuntimeResourceDefinition def = theFhirContext.getResourceDefinition(theResource);
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BaseRuntimeChildDefinition base = def.getChildByName(theChildName);
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return base
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.getAccessor()
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.getFirstValueOrNull(theResource)
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.map(t -> ((IPrimitiveType<?>) t))
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.map(t -> t.getValueAsString())
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.orElse(null);
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}
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}
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@ -90,6 +90,7 @@ import ca.uhn.fhir.validation.IValidatorModule;
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import ca.uhn.fhir.validation.ValidationOptions;
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import ca.uhn.fhir.validation.ValidationResult;
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import org.apache.commons.lang3.Validate;
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import org.apache.commons.text.WordUtils;
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import org.hl7.fhir.instance.model.api.IBaseCoding;
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import org.hl7.fhir.instance.model.api.IBaseMetaType;
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import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
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@ -123,7 +124,10 @@ import java.util.List;
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import java.util.Optional;
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import java.util.Set;
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import java.util.UUID;
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import java.util.regex.Pattern;
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import java.util.stream.Collectors;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends BaseHapiFhirDao<T> implements IFhirResourceDao<T> {
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@ -761,8 +765,16 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
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}
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if (myDaoConfig.isMarkResourcesForReindexingUponSearchParameterChange()) {
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if (isNotBlank(theExpression) && theExpression.contains(".")) {
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final String resourceType = theExpression.substring(0, theExpression.indexOf('.'));
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String expression = defaultString(theExpression);
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Set<String> typesToMark = myDaoRegistry
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.getRegisteredDaoTypes()
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.stream()
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.filter(t -> WordUtils.containsAllWords(expression, t))
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.collect(Collectors.toSet());
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for (String resourceType : typesToMark) {
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ourLog.debug("Marking all resources of type {} for reindexing due to updated search parameter with path: {}", resourceType, theExpression);
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TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager);
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@ -774,6 +786,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
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ourLog.debug("Marked resources of type {} for reindexing", resourceType);
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}
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}
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mySearchParamRegistry.requestRefresh();
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@ -89,9 +89,30 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
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}
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public static void validateSearchParam(ISearchParamRegistry theSearchParamRegistry, ISearchParamExtractor theSearchParamExtractor, String theCode, Enum<?> theType, Enum<?> theStatus, List<? extends IPrimitiveType> theBase, String theExpression, FhirContext theContext, DaoConfig theDaoConfig) {
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/*
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* If overriding built-in SPs is disabled on this server, make sure we aren't
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* doing that
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*/
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if (theDaoConfig.getModelConfig().isDefaultSearchParamsCanBeOverridden() == false) {
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for (IPrimitiveType<?> nextBaseType : theBase) {
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String nextBase = nextBaseType.getValueAsString();
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RuntimeSearchParam existingSearchParam = theSearchParamRegistry.getActiveSearchParam(nextBase, theCode);
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if (existingSearchParam != null && existingSearchParam.getId() == null) {
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throw new UnprocessableEntityException("Can not override built-in search parameter " + nextBase + ":" + theCode + " because overriding is disabled on this server");
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}
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}
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}
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/*
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* Everything below is validating that the SP is actually valid. We'll only do that if the
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* SPO is active, so that we don't block people from uploading works-in-progress
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*/
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if (theStatus == null) {
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throw new UnprocessableEntityException("SearchParameter.status is missing or invalid");
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}
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if (!theStatus.name().equals("ACTIVE")) {
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return;
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}
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if (ElementUtil.isEmpty(theBase) && (theType == null || !Enumerations.SearchParamType.COMPOSITE.name().equals(theType.name()))) {
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throw new UnprocessableEntityException("SearchParameter.base is missing");
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@ -150,18 +171,6 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
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}
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} // if have expression
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// If overriding built-in SPs is disabled on this server, make sure we aren't
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// doing that
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if (theDaoConfig.getModelConfig().isDefaultSearchParamsCanBeOverridden() == false) {
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for (IPrimitiveType<?> nextBaseType : theBase) {
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String nextBase = nextBaseType.getValueAsString();
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RuntimeSearchParam existingSearchParam = theSearchParamRegistry.getActiveSearchParam(nextBase, theCode);
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if (existingSearchParam != null && existingSearchParam.getId() == null) {
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throw new UnprocessableEntityException("Can not override built-in search parameter " + nextBase + ":" + theCode + " because overriding is disabled on this server");
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}
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}
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}
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}
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}
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@ -33,6 +33,8 @@ 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.InternalErrorException;
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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 com.google.common.annotations.VisibleForTesting;
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import com.google.common.collect.Lists;
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import com.google.gson.Gson;
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import com.google.gson.JsonElement;
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@ -55,6 +57,9 @@ import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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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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*/
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@ -73,9 +78,9 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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boolean enabled = true;
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@Autowired
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private FhirContext fhirContext;
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private FhirContext myFhirContext;
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@Autowired
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private DaoRegistry daoRegistry;
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private DaoRegistry myDaoRegistry;
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@Autowired
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private IValidationSupport validationSupport;
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@Autowired
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@ -90,7 +95,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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@PostConstruct
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public void initialize() {
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switch (fhirContext.getVersion().getVersion()) {
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switch (myFhirContext.getVersion().getVersion()) {
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case R5:
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case R4:
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case DSTU3:
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@ -100,7 +105,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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case DSTU2_HL7ORG:
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case DSTU2_1:
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default: {
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ourLog.info("IG installation not supported for version: {}", fhirContext.getVersion().getVersion());
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ourLog.info("IG installation not supported for version: {}", myFhirContext.getVersion().getVersion());
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enabled = false;
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}
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}
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@ -159,7 +164,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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String version = npmPackage.getNpm().get("version").getAsString();
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String fhirVersion = npmPackage.fhirVersion();
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String currentFhirVersion = fhirContext.getVersion().getVersion().getFhirVersionString();
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String currentFhirVersion = myFhirContext.getVersion().getVersion().getFhirVersionString();
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assertFhirVersionsAreCompatible(fhirVersion, currentFhirVersion);
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List<String> installTypes;
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@ -264,9 +269,9 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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for (String file : filesForType) {
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try {
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byte[] content = pkg.getFolders().get("package").fetchFile(file);
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resources.add(fhirContext.newJsonParser().parseResource(new String(content)));
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resources.add(myFhirContext.newJsonParser().parseResource(new String(content)));
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} catch (IOException e) {
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throw new InternalErrorException("Cannot install resource of type "+type+": Could not fetch file "+ file, e);
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throw new InternalErrorException("Cannot install resource of type " + type + ": Could not fetch file " + file, e);
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}
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}
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}
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@ -277,10 +282,14 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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* Create a resource or update it, if its already existing.
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*/
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private void createOrUpdate(IBaseResource resource) {
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IFhirResourceDao dao = daoRegistry.getResourceDao(resource.getClass());
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IFhirResourceDao dao = myDaoRegistry.getResourceDao(resource.getClass());
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IBundleProvider searchResult = dao.search(createSearchParameterMapFor(resource));
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if (searchResult.isEmpty()) {
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dao.create(resource);
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if (validForUpload(resource)) {
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dao.create(resource);
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}
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} else {
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IBaseResource existingResource = verifySearchResultFor(resource, searchResult);
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if (existingResource != null) {
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@ -290,8 +299,30 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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}
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}
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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 (defaultString(code).startsWith("_")) {
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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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return false;
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}
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if (SearchParameterUtil.getBaseAsStrings(myFhirContext, theResource).isEmpty()) {
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return false;
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}
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}
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return true;
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}
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private boolean isStructureDefinitionWithoutSnapshot(IBaseResource r) {
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FhirTerser terser = fhirContext.newTerser();
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FhirTerser terser = myFhirContext.newTerser();
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return r.getClass().getSimpleName().equals("StructureDefinition") &&
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terser.getSingleValueOrNull(r, "snapshot") == null;
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}
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@ -319,7 +350,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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}
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private IBaseResource verifySearchResultFor(IBaseResource resource, IBundleProvider searchResult) {
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FhirTerser terser = fhirContext.newTerser();
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FhirTerser terser = myFhirContext.newTerser();
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if (resource.getClass().getSimpleName().equals("NamingSystem")) {
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if (searchResult.size() > 1) {
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ourLog.warn("Expected 1 NamingSystem with unique ID {}, found {}. Will not attempt to update resource.",
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@ -346,7 +377,7 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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}
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private String extractUniqeIdFromNamingSystem(IBaseResource resource) {
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FhirTerser terser = fhirContext.newTerser();
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FhirTerser terser = myFhirContext.newTerser();
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IBase uniqueIdComponent = (IBase) terser.getSingleValueOrNull(resource, "uniqueId");
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if (uniqueIdComponent == null) {
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throw new ImplementationGuideInstallationException("NamingSystem does not have uniqueId component.");
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@ -356,17 +387,22 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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}
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private String extractIdFromSubscription(IBaseResource resource) {
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FhirTerser terser = fhirContext.newTerser();
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FhirTerser terser = myFhirContext.newTerser();
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IPrimitiveType asPrimitiveType = (IPrimitiveType) terser.getSingleValueOrNull(resource, "id");
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return (String) asPrimitiveType.getValue();
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}
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private String extractUniqueUrlFromMetadataResouce(IBaseResource resource) {
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FhirTerser terser = fhirContext.newTerser();
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FhirTerser terser = myFhirContext.newTerser();
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IPrimitiveType asPrimitiveType = (IPrimitiveType) terser.getSingleValueOrNull(resource, "url");
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return (String) asPrimitiveType.getValue();
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}
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@VisibleForTesting
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void setFhirContextForUnitTest(FhirContext theCtx) {
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myFhirContext = theCtx;
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}
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private static IBaseResource getFirstResourceFrom(IBundleProvider searchResult) {
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try {
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return searchResult.getResources(0, 0).get(0);
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@ -1605,6 +1605,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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if (element.hasTarget()) {
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TermConceptMapGroupElementTarget termConceptMapGroupElementTarget;
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for (ConceptMap.TargetElementComponent elementTarget : element.getTarget()) {
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if (isBlank(elementTarget.getCode())) {
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continue;
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}
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termConceptMapGroupElementTarget = new TermConceptMapGroupElementTarget();
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termConceptMapGroupElementTarget.setConceptMapGroupElement(termConceptMapGroupElement);
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termConceptMapGroupElementTarget.setCode(elementTarget.getCode());
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@ -1086,6 +1086,51 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
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}
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/**
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* Handle ConceptMaps where targets are missing, such as this one:
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*
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* https://www.hl7.org/fhir/conceptmap-example-specimen-type.html
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*/
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@Test
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public void testUploadConceptMapWithMappingTargetsMissing() {
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ConceptMap cm = new ConceptMap();
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cm.setUrl("http://foo");
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cm.setSource(new CanonicalType("http://source"));
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cm.setTarget(new CanonicalType("http://target"));
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cm.addGroup().addElement().setCode("source1").addTarget().setCode("target1").setEquivalence(ConceptMapEquivalence.EQUAL);
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cm.addGroup().addElement().setCode("source2"); // no target
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cm.addGroup().addElement().setCode("source3").addTarget().setComment("No target code"); // no target code
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myConceptMapDao.create(cm);
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runInTransaction(()->{
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TranslationRequest translationRequest = new TranslationRequest();
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translationRequest.getCodeableConcept().addCoding()
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.setSystem("http://source")
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.setCode("source1");
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translationRequest.setTarget(new UriType("http://target"));
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ourLog.info("*** About to translate");
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TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
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ourLog.info("*** Done translating");
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assertTrue(translationResult.getResult().booleanValue());
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assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
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assertEquals(1, translationResult.getMatches().size());
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TranslationMatch translationMatch = translationResult.getMatches().get(0);
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assertEquals("equal", translationMatch.getEquivalence().getCode());
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Coding concept = translationMatch.getConcept();
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assertEquals("target1", concept.getCode());
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assertEquals(null, concept.getDisplay());
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assertEquals("http://target", concept.getSystem());
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});
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}
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@Test
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public void testUploadAndApplyR4DemoConceptMap() throws IOException {
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@ -91,6 +91,46 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
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public void beforeDisableResultReuse() {
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myDaoConfig.setReuseCachedSearchResultsForMillis(null);
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myModelConfig.setDefaultSearchParamsCanBeOverridden(new ModelConfig().isDefaultSearchParamsCanBeOverridden());
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myDaoConfig.setMarkResourcesForReindexingUponSearchParameterChange(new DaoConfig().isMarkResourcesForReindexingUponSearchParameterChange());
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}
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@Test
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public void testStoreSearchParamWithBracketsInExpression() {
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myDaoConfig.setMarkResourcesForReindexingUponSearchParameterChange(true);
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SearchParameter fooSp = new SearchParameter();
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fooSp.setCode("foo");
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fooSp.addBase("ActivityDefinition");
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fooSp.setType(Enumerations.SearchParamType.REFERENCE);
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fooSp.setTitle("FOO SP");
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fooSp.setExpression("(ActivityDefinition.useContext.value as Quantity) | (ActivityDefinition.useContext.value as Range)");
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fooSp.setXpathUsage(org.hl7.fhir.r4.model.SearchParameter.XPathUsageType.NORMAL);
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fooSp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE);
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// Ensure that no exceptions are thrown
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mySearchParameterDao.create(fooSp, mySrd);
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mySearchParamRegistry.forceRefresh();
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}
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/**
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* Draft search parameters should be ok even if they aren't completely valid
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*/
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@Test
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public void testStoreDraftSearchParam_DontValidate() {
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myDaoConfig.setMarkResourcesForReindexingUponSearchParameterChange(true);
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SearchParameter fooSp = new SearchParameter();
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fooSp.setCode("foo");
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fooSp.addBase("ActivityDefinition");
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fooSp.setType(Enumerations.SearchParamType.REFERENCE);
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fooSp.setTitle("FOO SP");
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fooSp.setExpression("FOO FOO FOO");
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fooSp.setXpathUsage(org.hl7.fhir.r4.model.SearchParameter.XPathUsageType.NORMAL);
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fooSp.setStatus(Enumerations.PublicationStatus.DRAFT);
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// Ensure that no exceptions are thrown
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mySearchParameterDao.create(fooSp, mySrd);
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mySearchParamRegistry.forceRefresh();
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}
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@ -27,6 +27,7 @@ import org.hl7.fhir.r4.model.StructureDefinition;
|
|||
import org.hl7.fhir.utilities.cache.NpmPackage;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Disabled;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
|
@ -95,6 +96,18 @@ public class NpmTestR4 extends BaseJpaR4Test {
|
|||
}
|
||||
|
||||
|
||||
@Disabled("This test is super slow so don't run by default")
|
||||
@Test
|
||||
public void testInstallUsCore() {
|
||||
JpaPackageCache jpaPackageCache = ProxyUtil.getSingletonTarget(myPackageCacheManager, JpaPackageCache.class);
|
||||
jpaPackageCache.getPackageServers().clear();
|
||||
jpaPackageCache.addPackageServer("https://packages.fhir.org");
|
||||
|
||||
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.us.core").setVersion("3.1.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL).setFetchDependencies(true);
|
||||
igInstaller.install(spec);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testCacheDstu3Package() throws Exception {
|
||||
byte[] bytes = loadClasspathBytes("/packages/nictiz.fhir.nl.stu3.questionnaires-1.0.2.tgz");
|
||||
|
|
|
|||
|
|
@ -0,0 +1,60 @@
|
|||
package ca.uhn.fhir.jpa.packages;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import org.hl7.fhir.r4.model.Enumerations;
|
||||
import org.hl7.fhir.r4.model.SearchParameter;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
class PackageInstallerSvcImplTest {
|
||||
private final FhirContext myCtx = FhirContext.forCached(FhirVersionEnum.R4);
|
||||
private PackageInstallerSvcImpl mySvc;
|
||||
|
||||
|
||||
@BeforeEach
|
||||
public void before() {
|
||||
mySvc = new PackageInstallerSvcImpl();
|
||||
mySvc.setFhirContextForUnitTest(myCtx);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidForUpload_SearchParameterWithMetaParam() {
|
||||
SearchParameter sp = new SearchParameter();
|
||||
sp.setCode("_id");
|
||||
assertFalse(mySvc.validForUpload(sp));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidForUpload_SearchParameterWithNoBase() {
|
||||
SearchParameter sp = new SearchParameter();
|
||||
sp.setCode("name");
|
||||
sp.setExpression("Patient.name");
|
||||
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
assertFalse(mySvc.validForUpload(sp));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidForUpload_SearchParameterWithNoExpression() {
|
||||
SearchParameter sp = new SearchParameter();
|
||||
sp.setCode("name");
|
||||
sp.addBase("Patient");
|
||||
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
assertFalse(mySvc.validForUpload(sp));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testValidForUpload_GoodSearchParameter() {
|
||||
SearchParameter sp = new SearchParameter();
|
||||
sp.setCode("name");
|
||||
sp.addBase("Patient");
|
||||
sp.setExpression("Patient.name");
|
||||
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
assertTrue(mySvc.validForUpload(sp));
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue