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Resolve 4863 from release branch searchparametercanonicalizer does not account for search parameters for custom resources types when converting dstu23 into runtimesearchparam #4887

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Merged
merged 9 commits into from
May 18, 2023
Merged

Resolve 4863 from release branch searchparametercanonicalizer does not account for search parameters for custom resources types when converting dstu23 into runtimesearchparam #4887

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f6c1451
Modified canonicalizeSearchParameterDstu2 and 3, now correctly detect…
TynerGjs May 12, 2023
d229f9f
Canonicalizers now correctly handle search parameters for custom reso…
TynerGjs May 15, 2023
e58d111
created changelog
TynerGjs May 15, 2023
1d684c5
Modification based on comments:
TynerGjs May 17, 2023
44b6926
Added tests for the SearchParameterCanonicalizer to test if base and …
TynerGjs May 17, 2023
c82447a
Fixed typo and removed commented code
TynerGjs May 17, 2023
51f7b95
re-ordered init methods
TynerGjs May 17, 2023
d0a20f8
Update changelog
TynerGjs May 17, 2023
c1142ea
modifications following first code review.
May 18, 2023
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252 changes: 125 additions & 127 deletions ...aram/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/SearchParameterCanonicalizer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,30 +27,48 @@
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.*;
import ca.uhn.fhir.util.DatatypeUtil;
import ca.uhn.fhir.util.ExtensionUtil;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.PhoneticEncoderUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.SearchParameter;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;

import java.util.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;

import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.startsWith;

@Service
public class SearchParameterCanonicalizer {
private static final Logger ourLog = LoggerFactory.getLogger(SearchParameterCanonicalizer.class);

private final FhirContext myFhirContext;

private final FhirTerser myTerser;
@Autowired
public SearchParameterCanonicalizer(FhirContext theFhirContext) {
myFhirContext = theFhirContext;
myTerser = myFhirContext.newTerser();
}

private static Collection<String> toStrings(Collection<? extends IPrimitiveType<String>> theBase) {
Expand Down Expand Up @@ -96,21 +114,11 @@ private RuntimeSearchParam canonicalizeSearchParameterDstu2(ca.uhn.fhir.model.ds
String description = theNextSp.getDescription();
String path = theNextSp.getXpath();

Collection<String> base = toStrings(Collections.singletonList(theNextSp.getBaseElement()));
// add extensions as base if the SP is for a custom resource type
List<ExtensionDt> customSPBase = theNextSp.getUndeclaredExtensionsByUrl(HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE);
ArrayList<String> baseFromExtensions = new ArrayList<>();
for (ExtensionDt e : customSPBase) {
String eStr = e.getValueAsPrimitive().getValueAsString();
if (StringUtils.isNotBlank(eStr)) {
baseFromExtensions.add(eStr);
}
}
// when base contains custom resources, "Resource" is present to satisfy 1...* cardinality requirement of FHIR
// removed it for RuntimeSearchParam
if (!baseFromExtensions.isEmpty()){
base.remove("Resource");
base.addAll(baseFromExtensions);
Collection<String> baseResource = toStrings(Collections.singletonList(theNextSp.getBaseElement()));
List<String> baseCustomResources = extractDstu2CustomResourcesFromExtensions(theNextSp, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE);

if(!baseCustomResources.isEmpty()){
baseResource = Collections.singleton(baseCustomResources.get(0));
}

RestSearchParameterTypeEnum paramType = null;
Expand Down Expand Up @@ -156,22 +164,11 @@ private RuntimeSearchParam canonicalizeSearchParameterDstu2(ca.uhn.fhir.model.ds
break;
}
}
Set<String> targets = DatatypeUtil.toStringSet(theNextSp.getTarget());
// add extensions as target if the SP is for a custom resource type
Set<String> targetsFromExtensions = new HashSet<>();
List<ExtensionDt> customSPTargets = theNextSp.getUndeclaredExtensionsByUrl(HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE);
for (ExtensionDt e : customSPTargets) {
String eStr = e.getValueAsPrimitive().getValueAsString();
if (StringUtils.isNotBlank(eStr)) {
targetsFromExtensions.add(eStr);
}
}
// when targets contains custom resources, "Resource" is present to satisfy 1...* cardinality requirement of FHIR
// removed it for RuntimeSearchParam
if (!targetsFromExtensions.isEmpty()){
targets.remove("Resource");
targets.addAll(targetsFromExtensions);
}

Set<String> targetResources = DatatypeUtil.toStringSet(theNextSp.getTarget());
List<String> targetCustomResources = extractDstu2CustomResourcesFromExtensions(theNextSp, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE);

maybeAddCustomResourcesToResources(targetResources, targetCustomResources);

if (isBlank(name) || isBlank(path)) {
if (paramType != RestSearchParameterTypeEnum.COMPOSITE) {
Expand All @@ -196,30 +193,18 @@ private RuntimeSearchParam canonicalizeSearchParameterDstu2(ca.uhn.fhir.model.ds
}

List<RuntimeSearchParam.Component> components = Collections.emptyList();
return new RuntimeSearchParam(id, uri, name, description, path, paramType, Collections.emptySet(), targets, status, unique, components, base);
return new RuntimeSearchParam(id, uri, name, description, path, paramType, Collections.emptySet(), targetResources, status, unique, components, baseResource);
}

private RuntimeSearchParam canonicalizeSearchParameterDstu3(org.hl7.fhir.dstu3.model.SearchParameter theNextSp) {
String name = theNextSp.getCode();
String description = theNextSp.getDescription();
String path = theNextSp.getExpression();

List<String> base = new ArrayList<>(toStrings(theNextSp.getBase()));
// add extensions as base if the SP is for a custom resource type
List<Extension> customSPBase = theNextSp.getExtensionsByUrl(HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE);
ArrayList<String> baseFromExtensions = new ArrayList<>();
for (Extension e : customSPBase){
String eStr = e.getValueAsPrimitive().getValueAsString();
if (StringUtils.isNotBlank(eStr)) {
baseFromExtensions.add(eStr);
}
}
// when base contains custom resources, "Resource" is present to satisfy 1...* cardinality requirement of FHIR
// removed it for RuntimeSearchParam
if (!baseFromExtensions.isEmpty()){
base.remove("Resource");
base.addAll(baseFromExtensions);
}
List<String> baseResources = new ArrayList<>(toStrings(theNextSp.getBase()));
List<String> baseCustomResources = extractDstu3CustomResourcesFromExtensions(theNextSp, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE);

maybeAddCustomResourcesToResources(baseResources, baseCustomResources);

RestSearchParameterTypeEnum paramType = null;
RuntimeSearchParam.RuntimeSearchParamStatusEnum status = null;
Expand Down Expand Up @@ -272,22 +257,10 @@ private RuntimeSearchParam canonicalizeSearchParameterDstu3(org.hl7.fhir.dstu3.m
}
}

Set<String> targets = DatatypeUtil.toStringSet(theNextSp.getTarget());
// add extensions as target if the SP is for a custom resource type
Set<String> targetsFromExtensions = new HashSet<>();
List<Extension> customSPTargets = theNextSp.getExtensionsByUrl(HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE);
for (Extension e : customSPTargets) {
String eStr = e.getValueAsPrimitive().getValueAsString();
if (StringUtils.isNotBlank(eStr)) {
targetsFromExtensions.add(eStr);
}
}
// when targets contains custom resources, "Resource" is present to satisfy 1...* cardinality requirement of FHIR
// removed it for RuntimeSearchParam
if (!targetsFromExtensions.isEmpty()){
targets.remove("Resource");
targets.addAll(targetsFromExtensions);
}
Set<String> targetResources = DatatypeUtil.toStringSet(theNextSp.getTarget());
List<String> targetCustomResources = extractDstu3CustomResourcesFromExtensions(theNextSp, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE);

maybeAddCustomResourcesToResources(targetResources, targetCustomResources);

if (isBlank(name) || isBlank(path) || paramType == null) {
if (paramType != RestSearchParameterTypeEnum.COMPOSITE) {
Expand Down Expand Up @@ -316,44 +289,23 @@ private RuntimeSearchParam canonicalizeSearchParameterDstu3(org.hl7.fhir.dstu3.m
components.add(new RuntimeSearchParam.Component(next.getExpression(), next.getDefinition().getReferenceElement().toUnqualifiedVersionless().getValue()));
}

return new RuntimeSearchParam(id, uri, name, description, path, paramType, Collections.emptySet(), targets, status, unique, components, base);
return new RuntimeSearchParam(id, uri, name, description, path, paramType, Collections.emptySet(), targetResources, status, unique, components, baseResources);
}

private RuntimeSearchParam canonicalizeSearchParameterR4Plus(IBaseResource theNextSp) {
FhirTerser terser = myFhirContext.newTerser();
String name = terser.getSinglePrimitiveValueOrNull(theNextSp, "code");
String description = terser.getSinglePrimitiveValueOrNull(theNextSp, "description");
String path = terser.getSinglePrimitiveValueOrNull(theNextSp, "expression");

String name = myTerser.getSinglePrimitiveValueOrNull(theNextSp, "code");
String description = myTerser.getSinglePrimitiveValueOrNull(theNextSp, "description");
String path = myTerser.getSinglePrimitiveValueOrNull(theNextSp, "expression");

List<String> base = terser
.getValues(theNextSp, "base", IPrimitiveType.class)
.stream()
.map(IPrimitiveType::getValueAsString)
.collect(Collectors.toList());
Set<String> baseResources = extractR4PlusResources("base", theNextSp);
List<String> baseCustomResources = extractR4PlusCustomResourcesFromExtensions(theNextSp, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE);

ArrayList<String> baseFromExtension = new ArrayList<>();
if (theNextSp instanceof IBaseHasExtensions) {
((IBaseHasExtensions) theNextSp)
.getExtension()
.stream()
.filter(t -> HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE.equals(t.getUrl()))
.filter(t -> t.getValue() instanceof IPrimitiveType)
.map(t -> ((IPrimitiveType<?>) t.getValue()))
.map(IPrimitiveType::getValueAsString)
.filter(StringUtils::isNotBlank)
.forEach(baseFromExtension::add);
}
// when base contains custom resources, "Resource" is present to satisfy 1...* cardinality requirement of FHIR
// removed it for RuntimeSearchParam
if (!baseFromExtension.isEmpty()){
base.remove("Resource");
base.addAll(baseFromExtension);
}
maybeAddCustomResourcesToResources(baseResources, baseCustomResources);

RestSearchParameterTypeEnum paramType = null;
RuntimeSearchParam.RuntimeSearchParamStatusEnum status = null;
switch (terser.getSinglePrimitiveValue(theNextSp, "type").orElse("")) {
switch (myTerser.getSinglePrimitiveValue(theNextSp, "type").orElse("")) {
case "composite":
paramType = RestSearchParameterTypeEnum.COMPOSITE;
break;
Expand Down Expand Up @@ -382,7 +334,7 @@ private RuntimeSearchParam canonicalizeSearchParameterR4Plus(IBaseResource theNe
paramType = RestSearchParameterTypeEnum.SPECIAL;
break;
}
switch (terser.getSinglePrimitiveValue(theNextSp, "status").orElse("")) {
switch (myTerser.getSinglePrimitiveValue(theNextSp, "status").orElse("")) {
case "active":
status = RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE;
break;
Expand All @@ -397,29 +349,10 @@ private RuntimeSearchParam canonicalizeSearchParameterR4Plus(IBaseResource theNe
break;
}

Set<String> targets = terser
.getValues(theNextSp, "target", IPrimitiveType.class)
.stream()
.map(IPrimitiveType::getValueAsString)
.collect(Collectors.toSet());
Set<String> targetsFromExtensions = new HashSet<>();
if (theNextSp instanceof IBaseHasExtensions) {
((IBaseHasExtensions) theNextSp)
.getExtension()
.stream()
.filter(t -> HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE.equals(t.getUrl()))
.filter(t -> t.getValue() instanceof IPrimitiveType)
.map(t -> ((IPrimitiveType<?>) t.getValue()))
.map(IPrimitiveType::getValueAsString)
.filter(StringUtils::isNotBlank)
.forEach(targetsFromExtensions::add);
}
// when targets contains custom resources, "Resource" is present to satisfy 1...* cardinality requirement of FHIR
// removed it for RuntimeSearchParam
if(!targetsFromExtensions.isEmpty()){
targets.remove("Resource");
targets.addAll(targetsFromExtensions);
}
Set<String> targetResources = extractR4PlusResources("target", theNextSp);
List<String> targetCustomResources = extractR4PlusCustomResourcesFromExtensions(theNextSp, HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE);

maybeAddCustomResourcesToResources(targetResources, targetCustomResources);

if (isBlank(name) || isBlank(path) || paramType == null) {
if ("_text".equals(name) || "_content".equals(name)) {
Expand All @@ -430,7 +363,7 @@ private RuntimeSearchParam canonicalizeSearchParameterR4Plus(IBaseResource theNe
}

IIdType id = theNextSp.getIdElement();
String uri = terser.getSinglePrimitiveValueOrNull(theNextSp, "url");
String uri = myTerser.getSinglePrimitiveValueOrNull(theNextSp, "url");
ComboSearchParamType unique = null;

String value = ((IBaseHasExtensions) theNextSp).getExtension()
Expand All @@ -448,17 +381,25 @@ private RuntimeSearchParam canonicalizeSearchParameterR4Plus(IBaseResource theNe
}

List<RuntimeSearchParam.Component> components = new ArrayList<>();
for (IBase next : terser.getValues(theNextSp, "component")) {
String expression = terser.getSinglePrimitiveValueOrNull(next, "expression");
String definition = terser.getSinglePrimitiveValueOrNull(next, "definition");
for (IBase next : myTerser.getValues(theNextSp, "component")) {
String expression = myTerser.getSinglePrimitiveValueOrNull(next, "expression");
String definition = myTerser.getSinglePrimitiveValueOrNull(next, "definition");
if (startsWith(definition, "/SearchParameter/")) {
definition = definition.substring(1);
}

components.add(new RuntimeSearchParam.Component(expression, definition));
}

return new RuntimeSearchParam(id, uri, name, description, path, paramType, Collections.emptySet(), targets, status, unique, components, base);
return new RuntimeSearchParam(id, uri, name, description, path, paramType, Collections.emptySet(), targetResources, status, unique, components, baseResources);
}

private Set<String> extractR4PlusResources(String thePath, IBaseResource theNextSp) {
return myTerser
.getValues(theNextSp, thePath, IPrimitiveType.class)
.stream()
.map(IPrimitiveType::getValueAsString)
.collect(Collectors.toSet());
}

/**
Expand Down Expand Up @@ -506,5 +447,62 @@ private void setEncoder(RuntimeSearchParam theRuntimeSearchParam, IBaseDatatype
}
}

private List<String> extractDstu2CustomResourcesFromExtensions(ca.uhn.fhir.model.dstu2.resource.SearchParameter theSearchParameter, String theExtensionUrl) {

List<ExtensionDt> customSpExtensionDt = theSearchParameter.getUndeclaredExtensionsByUrl(theExtensionUrl);

return customSpExtensionDt.stream()
.map(theExtensionDt -> theExtensionDt.getValueAsPrimitive().getValueAsString())
.filter(StringUtils::isNotBlank)
.collect(Collectors.toList());
}

private List<String> extractDstu3CustomResourcesFromExtensions(org.hl7.fhir.dstu3.model.SearchParameter theSearchParameter, String theExtensionUrl) {

List<Extension> customSpExtensions = theSearchParameter.getExtensionsByUrl(theExtensionUrl);

return customSpExtensions.stream()
.map(theExtension -> theExtension.getValueAsPrimitive().getValueAsString())
.filter(StringUtils::isNotBlank)
.collect(Collectors.toList());

}

private List<String> extractR4PlusCustomResourcesFromExtensions(IBaseResource theSearchParameter, String theExtensionUrl) {

List<String> retVal = new ArrayList<>();

if (theSearchParameter instanceof IBaseHasExtensions) {
((IBaseHasExtensions) theSearchParameter)
.getExtension()
.stream()
.filter(t -> theExtensionUrl.equals(t.getUrl()))
.filter(t -> t.getValue() instanceof IPrimitiveType)
.map(t -> ((IPrimitiveType<?>) t.getValue()))
.map(IPrimitiveType::getValueAsString)
.filter(StringUtils::isNotBlank)
.forEach(retVal::add);
}

return retVal;
}

private <T extends Collection<String>> void maybeAddCustomResourcesToResources(T theResources, List<String> theCustomResources) {
// SearchParameter base and target components require strict binding to ResourceType for dstu[2|3], R4, R4B
// and to Version Independent Resource Types for R5.
//
// To handle custom resources, we set a placeholder of type 'Resource' in the base or target component and define
// the custom resource by adding a corresponding extension with url HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_BASE_RESOURCE
// or HapiExtensions.EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE with the name of the custom resource.
//
// To provide a base/target list that contains both the resources and customResources, we need to remove the placeholders
// from the theResources and add theCustomResources.

if (!theCustomResources.isEmpty()){
theResources.removeAll(Collections.singleton("Resource"));
theResources.addAll(theCustomResources);
}

}

}