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Builds the hapi fhir base. Requires Common lang, commons-text, and guava be built first.
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.parser;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
import ca.uhn.fhir.context.RuntimeChildContainedResources;
import ca.uhn.fhir.context.RuntimeChildNarrativeDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.IIdentifiableElement;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.parser.path.EncodeContextPath;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.MetaUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import jakarta.annotation.Nullable;
import org.apache.commons.io.output.StringBuilderWriter;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseElement;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions;
import org.hl7.fhir.instance.model.api.IBaseMetaType;
import org.hl7.fhir.instance.model.api.IBaseReference;
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 java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.io.Writer;
import java.lang.reflect.Modifier;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.startsWith;
@SuppressWarnings("WeakerAccess")
public abstract class BaseParser implements IParser {
/**
* Any resources that were created by the parser (i.e. by parsing a serialized resource) will have
* a {@link IBaseResource#getUserData(String) user data} property with this key.
*
* @since 5.0.0
*/
public static final String RESOURCE_CREATED_BY_PARSER =
BaseParser.class.getName() + "_" + "RESOURCE_CREATED_BY_PARSER";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
private static final Set notEncodeForContainedResource =
new HashSet<>(Arrays.asList("security", "versionId", "lastUpdated"));
private FhirTerser.ContainedResources myContainedResources;
private boolean myEncodeElementsAppliesToChildResourcesOnly;
private final FhirContext myContext;
private List myDontEncodeElements;
private List myEncodeElements;
private Set myEncodeElementsAppliesToResourceTypes;
private IIdType myEncodeForceResourceId;
private IParserErrorHandler myErrorHandler;
private boolean myOmitResourceId;
private List> myPreferTypes;
private String myServerBaseUrl;
private Boolean myStripVersionsFromReferences;
private Boolean myOverrideResourceIdWithBundleEntryFullUrl;
private boolean mySummaryMode;
private boolean mySuppressNarratives;
private Set myDontStripVersionsFromReferencesAtPaths;
/**
* Constructor
*/
public BaseParser(FhirContext theContext, IParserErrorHandler theParserErrorHandler) {
myContext = theContext;
myErrorHandler = theParserErrorHandler;
}
protected FhirContext getContext() {
return myContext;
}
List getDontEncodeElements() {
return myDontEncodeElements;
}
@Override
public IParser setDontEncodeElements(Collection theDontEncodeElements) {
if (theDontEncodeElements == null || theDontEncodeElements.isEmpty()) {
myDontEncodeElements = null;
} else {
myDontEncodeElements =
theDontEncodeElements.stream().map(EncodeContextPath::new).collect(Collectors.toList());
}
return this;
}
List getEncodeElements() {
return myEncodeElements;
}
@Override
public IParser setEncodeElements(Set theEncodeElements) {
if (theEncodeElements == null || theEncodeElements.isEmpty()) {
myEncodeElements = null;
myEncodeElementsAppliesToResourceTypes = null;
} else {
myEncodeElements =
theEncodeElements.stream().map(EncodeContextPath::new).collect(Collectors.toList());
myEncodeElementsAppliesToResourceTypes = new HashSet<>();
for (String next : myEncodeElements.stream()
.map(t -> t.getPath().get(0).getName())
.collect(Collectors.toList())) {
if (next.startsWith("*")) {
myEncodeElementsAppliesToResourceTypes = null;
break;
}
int dotIdx = next.indexOf('.');
if (dotIdx == -1) {
myEncodeElementsAppliesToResourceTypes.add(next);
} else {
myEncodeElementsAppliesToResourceTypes.add(next.substring(0, dotIdx));
}
}
}
return this;
}
protected Iterable compositeChildIterator(
IBase theCompositeElement,
final boolean theContainedResource,
final CompositeChildElement theParent,
EncodeContext theEncodeContext) {
BaseRuntimeElementCompositeDefinition elementDef = (BaseRuntimeElementCompositeDefinition)
myContext.getElementDefinition(theCompositeElement.getClass());
return theEncodeContext
.getCompositeChildrenCache()
.computeIfAbsent(new Key(elementDef, theContainedResource, theParent, theEncodeContext), (k) -> {
final List children = elementDef.getChildrenAndExtension();
final List result = new ArrayList<>(children.size());
for (final BaseRuntimeChildDefinition child : children) {
CompositeChildElement myNext = new CompositeChildElement(theParent, child, theEncodeContext);
/*
* There are lots of reasons we might skip encoding a particular child
*/
if (myNext.getDef().getElementName().equals("id")) {
continue;
} else if (!myNext.shouldBeEncoded(theContainedResource)) {
continue;
} else if (myNext.getDef() instanceof RuntimeChildNarrativeDefinition) {
if (isSuppressNarratives() || isSummaryMode()) {
continue;
}
} else if (myNext.getDef() instanceof RuntimeChildContainedResources) {
if (theContainedResource) {
continue;
}
}
result.add(myNext);
}
return result;
});
}
private String determineReferenceText(
IBaseReference theRef, CompositeChildElement theCompositeChildElement, IBaseResource theResource) {
IIdType ref = theRef.getReferenceElement();
if (isBlank(ref.getIdPart())) {
String reference = ref.getValue();
if (theRef.getResource() != null) {
IIdType containedId = getContainedResources().getResourceId(theRef.getResource());
if (containedId != null && !containedId.isEmpty()) {
if (containedId.isLocal()) {
reference = containedId.getValue();
} else {
reference = "#" + containedId.getValue();
}
} else {
IIdType refId = theRef.getResource().getIdElement();
if (refId != null) {
if (refId.hasIdPart()) {
if (refId.getValue().startsWith("urn:")) {
reference = refId.getValue();
} else {
if (!refId.hasResourceType()) {
refId = refId.withResourceType(myContext
.getResourceDefinition(theRef.getResource())
.getName());
}
if (isStripVersionsFromReferences(theCompositeChildElement, theResource)) {
reference = refId.toVersionless().getValue();
} else {
reference = refId.getValue();
}
}
}
}
}
}
return reference;
}
if (!ref.hasResourceType() && !ref.isLocal() && theRef.getResource() != null) {
ref = ref.withResourceType(
myContext.getResourceDefinition(theRef.getResource()).getName());
}
if (isNotBlank(myServerBaseUrl) && StringUtils.equals(myServerBaseUrl, ref.getBaseUrl())) {
if (isStripVersionsFromReferences(theCompositeChildElement, theResource)) {
return ref.toUnqualifiedVersionless().getValue();
}
return ref.toUnqualified().getValue();
}
if (isStripVersionsFromReferences(theCompositeChildElement, theResource)) {
return ref.toVersionless().getValue();
}
return ref.getValue();
}
protected abstract void doEncodeResourceToWriter(
IBaseResource theResource, Writer theWriter, EncodeContext theEncodeContext)
throws IOException, DataFormatException;
protected void doEncodeToWriter(IBase theElement, Writer theWriter, EncodeContext theEncodeContext)
throws IOException, DataFormatException {
throw new InternalErrorException(Msg.code(2363) + "This parser does not support encoding non-resource values");
}
protected abstract T doParseResource(Class theResourceType, Reader theReader)
throws DataFormatException;
@Override
public String encodeResourceToString(IBaseResource theResource) throws DataFormatException {
Writer stringWriter = new StringBuilderWriter();
try {
encodeResourceToWriter(theResource, stringWriter);
} catch (IOException e) {
throw new Error(
Msg.code(1828) + "Encountered IOException during write to string - This should not happen!", e);
}
return stringWriter.toString();
}
@Override
public final void encodeResourceToWriter(IBaseResource theResource, Writer theWriter)
throws IOException, DataFormatException {
EncodeContext encodeContext = new EncodeContext();
encodeResourceToWriter(theResource, theWriter, encodeContext);
}
@Override
public String encodeToString(IBase theElement) throws DataFormatException {
Writer stringWriter = new StringBuilderWriter();
try {
encodeToWriter(theElement, stringWriter);
} catch (IOException e) {
throw new Error(
Msg.code(2364) + "Encountered IOException during write to string - This should not happen!", e);
}
return stringWriter.toString();
}
@Override
public void encodeToWriter(IBase theElement, Writer theWriter) throws DataFormatException, IOException {
if (theElement instanceof IBaseResource) {
encodeResourceToWriter((IBaseResource) theElement, theWriter);
} else if (theElement instanceof IPrimitiveType) {
theWriter.write(((IPrimitiveType) theElement).getValueAsString());
} else {
EncodeContext encodeContext = new EncodeContext();
encodeToWriter(theElement, theWriter, encodeContext);
}
}
protected void encodeResourceToWriter(IBaseResource theResource, Writer theWriter, EncodeContext theEncodeContext)
throws IOException {
Validate.notNull(theResource, "theResource can not be null");
Validate.notNull(theWriter, "theWriter can not be null");
Validate.notNull(theEncodeContext, "theEncodeContext can not be null");
if (theResource.getStructureFhirVersionEnum() != myContext.getVersion().getVersion()) {
throw new IllegalArgumentException(Msg.code(1829) + "This parser is for FHIR version "
+ myContext.getVersion().getVersion() + " - Can not encode a structure for version "
+ theResource.getStructureFhirVersionEnum());
}
String resourceName =
myContext.getElementDefinition(theResource.getClass()).getName();
theEncodeContext.pushPath(resourceName, true);
doEncodeResourceToWriter(theResource, theWriter, theEncodeContext);
theEncodeContext.popPath();
}
protected void encodeToWriter(IBase theElement, Writer theWriter, EncodeContext theEncodeContext)
throws IOException {
Validate.notNull(theElement, "theElement can not be null");
Validate.notNull(theWriter, "theWriter can not be null");
Validate.notNull(theEncodeContext, "theEncodeContext can not be null");
BaseRuntimeElementDefinition def = myContext.getElementDefinition(theElement.getClass());
String elementName = def.getName();
theEncodeContext.pushPath(elementName, true);
doEncodeToWriter(theElement, theWriter, theEncodeContext);
theEncodeContext.popPath();
}
private void filterCodingsWithNoCodeOrSystem(List tagList) {
for (int i = 0; i < tagList.size(); i++) {
if (isBlank(tagList.get(i).getCode()) && isBlank(tagList.get(i).getSystem())) {
tagList.remove(i);
i--;
}
}
}
protected IIdType fixContainedResourceId(String theValue) {
IIdType retVal = (IIdType) myContext.getElementDefinition("id").newInstance();
if (StringUtils.isNotBlank(theValue) && theValue.charAt(0) == '#') {
retVal.setValue(theValue.substring(1));
} else {
retVal.setValue(theValue);
}
return retVal;
}
@SuppressWarnings("unchecked")
ChildNameAndDef getChildNameAndDef(BaseRuntimeChildDefinition theChild, IBase theValue) {
Class type = theValue.getClass();
String childName = theChild.getChildNameByDatatype(type);
BaseRuntimeElementDefinition childDef = theChild.getChildElementDefinitionByDatatype(type);
if (childDef == null) {
// if (theValue instanceof IBaseExtension) {
// return null;
// }
/*
* For RI structures Enumeration class, this replaces the child def
* with the "code" one. This is messy, and presumably there is a better
* way..
*/
BaseRuntimeElementDefinition elementDef = myContext.getElementDefinition(type);
if (elementDef.getName().equals("code")) {
Class type2 =
myContext.getElementDefinition("code").getImplementingClass();
childDef = theChild.getChildElementDefinitionByDatatype(type2);
childName = theChild.getChildNameByDatatype(type2);
}
// See possibly the user has extended a built-in type without
// declaring it anywhere, as in XmlParserDstu3Test#testEncodeUndeclaredBlock
if (childDef == null) {
Class nextSuperType = theValue.getClass();
while (IBase.class.isAssignableFrom(nextSuperType) && childDef == null) {
if (Modifier.isAbstract(nextSuperType.getModifiers()) == false) {
BaseRuntimeElementDefinition def =
myContext.getElementDefinition((Class) nextSuperType);
Class nextChildType = def.getImplementingClass();
childDef = theChild.getChildElementDefinitionByDatatype((Class) nextChildType);
childName = theChild.getChildNameByDatatype((Class) nextChildType);
}
nextSuperType = nextSuperType.getSuperclass();
}
}
if (childDef == null) {
throwExceptionForUnknownChildType(theChild, type);
}
}
return new ChildNameAndDef(childName, childDef);
}
protected String getCompositeElementId(IBase theElement) {
String elementId = null;
if (!(theElement instanceof IBaseResource)) {
if (theElement instanceof IBaseElement) {
elementId = ((IBaseElement) theElement).getId();
} else if (theElement instanceof IIdentifiableElement) {
elementId = ((IIdentifiableElement) theElement).getElementSpecificId();
}
}
return elementId;
}
FhirTerser.ContainedResources getContainedResources() {
return myContainedResources;
}
@Override
public Set getDontStripVersionsFromReferencesAtPaths() {
return myDontStripVersionsFromReferencesAtPaths;
}
@Override
public IIdType getEncodeForceResourceId() {
return myEncodeForceResourceId;
}
@Override
public BaseParser setEncodeForceResourceId(IIdType theEncodeForceResourceId) {
myEncodeForceResourceId = theEncodeForceResourceId;
return this;
}
protected IParserErrorHandler getErrorHandler() {
return myErrorHandler;
}
protected List, Object>> getExtensionMetadataKeys(IResource resource) {
List, Object>> extensionMetadataKeys = new ArrayList<>();
for (Map.Entry, Object> entry :
resource.getResourceMetadata().entrySet()) {
if (entry.getKey() instanceof ResourceMetadataKeyEnum.ExtensionResourceMetadataKey) {
extensionMetadataKeys.add(entry);
}
}
return extensionMetadataKeys;
}
protected String getExtensionUrl(final String extensionUrl) {
String url = extensionUrl;
if (StringUtils.isNotBlank(extensionUrl) && StringUtils.isNotBlank(myServerBaseUrl)) {
url = !UrlUtil.isValid(extensionUrl) && extensionUrl.startsWith("/")
? myServerBaseUrl + extensionUrl
: extensionUrl;
}
return url;
}
protected TagList getMetaTagsForEncoding(IResource theIResource, EncodeContext theEncodeContext) {
TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(theIResource);
if (shouldAddSubsettedTag(theEncodeContext)) {
tags = new TagList(tags);
tags.add(new Tag(getSubsettedCodeSystem(), Constants.TAG_SUBSETTED_CODE, subsetDescription()));
}
return tags;
}
@Override
public List> getPreferTypes() {
return myPreferTypes;
}
@Override
public void setPreferTypes(List> thePreferTypes) {
if (thePreferTypes != null) {
ArrayList> types = new ArrayList<>();
for (Class next : thePreferTypes) {
if (Modifier.isAbstract(next.getModifiers()) == false) {
types.add(next);
}
}
myPreferTypes = Collections.unmodifiableList(types);
} else {
myPreferTypes = thePreferTypes;
}
}
@SuppressWarnings("deprecation")
protected > List getProfileTagsForEncoding(
IBaseResource theResource, List theProfiles) {
switch (myContext.getAddProfileTagWhenEncoding()) {
case NEVER:
return theProfiles;
case ONLY_FOR_CUSTOM:
RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
if (resDef.isStandardType()) {
return theProfiles;
}
break;
case ALWAYS:
break;
}
RuntimeResourceDefinition nextDef = myContext.getResourceDefinition(theResource);
String profile = nextDef.getResourceProfile(myServerBaseUrl);
if (isNotBlank(profile)) {
for (T next : theProfiles) {
if (profile.equals(next.getValue())) {
return theProfiles;
}
}
List newList = new ArrayList<>(theProfiles);
BaseRuntimeElementDefinition idElement = myContext.getElementDefinition("id");
@SuppressWarnings("unchecked")
T newId = (T) idElement.newInstance();
newId.setValue(profile);
newList.add(newId);
return newList;
}
return theProfiles;
}
protected String getServerBaseUrl() {
return myServerBaseUrl;
}
@Override
public Boolean getStripVersionsFromReferences() {
return myStripVersionsFromReferences;
}
/**
* If set to true (default is false), narratives will not be included in the encoded
* values.
*
* @deprecated Use {@link #isSuppressNarratives()}
*/
@Deprecated
public boolean getSuppressNarratives() {
return mySuppressNarratives;
}
protected boolean isChildContained(BaseRuntimeElementDefinition childDef, boolean theIncludedResource) {
return (childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES
|| childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCE_LIST)
&& getContainedResources().isEmpty() == false
&& theIncludedResource == false;
}
@Override
public boolean isEncodeElementsAppliesToChildResourcesOnly() {
return myEncodeElementsAppliesToChildResourcesOnly;
}
@Override
public void setEncodeElementsAppliesToChildResourcesOnly(boolean theEncodeElementsAppliesToChildResourcesOnly) {
myEncodeElementsAppliesToChildResourcesOnly = theEncodeElementsAppliesToChildResourcesOnly;
}
@Override
public boolean isOmitResourceId() {
return myOmitResourceId;
}
private boolean isOverrideResourceIdWithBundleEntryFullUrl() {
Boolean overrideResourceIdWithBundleEntryFullUrl = myOverrideResourceIdWithBundleEntryFullUrl;
if (overrideResourceIdWithBundleEntryFullUrl != null) {
return overrideResourceIdWithBundleEntryFullUrl;
}
return myContext.getParserOptions().isOverrideResourceIdWithBundleEntryFullUrl();
}
private boolean isStripVersionsFromReferences(
CompositeChildElement theCompositeChildElement, IBaseResource theResource) {
Set autoVersionReferencesAtPathExtensions =
MetaUtil.getAutoVersionReferencesAtPath(theResource.getMeta(), myContext.getResourceType(theResource));
if (!autoVersionReferencesAtPathExtensions.isEmpty()
&& theCompositeChildElement.anyPathMatches(autoVersionReferencesAtPathExtensions)) {
return false;
}
Boolean stripVersionsFromReferences = myStripVersionsFromReferences;
if (stripVersionsFromReferences != null) {
return stripVersionsFromReferences;
}
if (myContext.getParserOptions().isStripVersionsFromReferences() == false) {
return false;
}
Set dontStripVersionsFromReferencesAtPaths = myDontStripVersionsFromReferencesAtPaths;
if (dontStripVersionsFromReferencesAtPaths != null) {
if (dontStripVersionsFromReferencesAtPaths.isEmpty() == false
&& theCompositeChildElement.anyPathMatches(dontStripVersionsFromReferencesAtPaths)) {
return false;
}
}
dontStripVersionsFromReferencesAtPaths =
myContext.getParserOptions().getDontStripVersionsFromReferencesAtPaths();
return dontStripVersionsFromReferencesAtPaths.isEmpty() != false
|| !theCompositeChildElement.anyPathMatches(dontStripVersionsFromReferencesAtPaths);
}
@Override
public boolean isSummaryMode() {
return mySummaryMode;
}
/**
* If set to true (default is false), narratives will not be included in the encoded
* values.
*
* @since 1.2
*/
public boolean isSuppressNarratives() {
return mySuppressNarratives;
}
@Override
public IBaseResource parseResource(InputStream theInputStream) throws DataFormatException {
return parseResource(new InputStreamReader(theInputStream, Charsets.UTF_8));
}
@Override
public T parseResource(Class theResourceType, InputStream theInputStream)
throws DataFormatException {
return parseResource(theResourceType, new InputStreamReader(theInputStream, Constants.CHARSET_UTF8));
}
@Override
public T parseResource(Class theResourceType, Reader theReader)
throws DataFormatException {
/*
* We do this so that the context can verify that the structure is for
* the correct FHIR version
*/
if (theResourceType != null) {
myContext.getResourceDefinition(theResourceType);
}
// Actually do the parse
T retVal = doParseResource(theResourceType, theReader);
RuntimeResourceDefinition def = myContext.getResourceDefinition(retVal);
if ("Bundle".equals(def.getName())) {
if (isOverrideResourceIdWithBundleEntryFullUrl()) {
BundleUtil.processEntries(myContext, (IBaseBundle) retVal, t -> {
String fullUrl = t.getFullUrl();
if (fullUrl != null) {
IBaseResource resource = t.getResource();
if (resource != null) {
IIdType resourceId = resource.getIdElement();
if (isBlank(resourceId.getValue())) {
resourceId.setValue(fullUrl);
} else {
if (fullUrl.startsWith("urn:")
&& fullUrl.length()
> resourceId.getIdPart().length()
&& fullUrl.charAt(fullUrl.length()
- resourceId.getIdPart().length()
- 1)
== ':'
&& fullUrl.endsWith(resourceId.getIdPart())) {
resourceId.setValue(fullUrl);
} else {
IIdType fullUrlId = myContext.getVersion().newIdType();
fullUrlId.setValue(fullUrl);
if (myContext.getVersion().getVersion().isOlderThan(FhirVersionEnum.DSTU3)) {
IIdType newId = fullUrlId;
if (!newId.hasVersionIdPart() && resourceId.hasVersionIdPart()) {
newId = newId.withVersion(resourceId.getVersionIdPart());
}
resourceId.setValue(newId.getValue());
} else if (StringUtils.equals(fullUrlId.getIdPart(), resourceId.getIdPart())) {
if (fullUrlId.hasBaseUrl()) {
IIdType newResourceId = resourceId.withServerBase(
fullUrlId.getBaseUrl(), resourceId.getResourceType());
resourceId.setValue(newResourceId.getValue());
}
}
}
}
}
}
});
}
}
return retVal;
}
@SuppressWarnings("cast")
@Override
public T parseResource(Class theResourceType, String theMessageString) {
StringReader reader = new StringReader(theMessageString);
return parseResource(theResourceType, reader);
}
@Override
public IBaseResource parseResource(Reader theReader) throws ConfigurationException, DataFormatException {
return parseResource(null, theReader);
}
@Override
public IBaseResource parseResource(String theMessageString) throws ConfigurationException, DataFormatException {
return parseResource(null, theMessageString);
}
protected List preProcessValues(
BaseRuntimeChildDefinition theMetaChildUncast,
IBaseResource theResource,
List theValues,
CompositeChildElement theCompositeChildElement,
EncodeContext theEncodeContext) {
if (myContext.getVersion().getVersion().isRi()) {
/*
* If we're encoding the meta tag, we do some massaging of the meta values before
* encoding. But if there is no meta element at all, we create one since we're possibly going to be
* adding things to it
*/
if (theValues.isEmpty() && theMetaChildUncast.getElementName().equals("meta")) {
BaseRuntimeElementDefinition metaChild = theMetaChildUncast.getChildByName("meta");
if (IBaseMetaType.class.isAssignableFrom(metaChild.getImplementingClass())) {
IBaseMetaType newType = (IBaseMetaType) metaChild.newInstance();
theValues = Collections.singletonList(newType);
}
}
if (theValues.size() == 1 && theValues.get(0) instanceof IBaseMetaType) {
IBaseMetaType metaValue = (IBaseMetaType) theValues.get(0);
try {
metaValue = (IBaseMetaType)
metaValue.getClass().getMethod("copy").invoke(metaValue);
} catch (Exception e) {
throw new InternalErrorException(Msg.code(1830) + "Failed to duplicate meta", e);
}
if (isBlank(metaValue.getVersionId())) {
if (theResource.getIdElement().hasVersionIdPart()) {
metaValue.setVersionId(theResource.getIdElement().getVersionIdPart());
}
}
filterCodingsWithNoCodeOrSystem(metaValue.getTag());
filterCodingsWithNoCodeOrSystem(metaValue.getSecurity());
List> newProfileList =
getProfileTagsForEncoding(theResource, metaValue.getProfile());
List> oldProfileList = metaValue.getProfile();
if (oldProfileList != newProfileList) {
oldProfileList.clear();
for (IPrimitiveType next : newProfileList) {
if (isNotBlank(next.getValue())) {
metaValue.addProfile(next.getValue());
}
}
}
if (shouldAddSubsettedTag(theEncodeContext)) {
IBaseCoding coding = metaValue.addTag();
coding.setCode(Constants.TAG_SUBSETTED_CODE);
coding.setSystem(getSubsettedCodeSystem());
coding.setDisplay(subsetDescription());
}
return Collections.singletonList(metaValue);
}
}
@SuppressWarnings("unchecked")
List retVal = (List) theValues;
for (int i = 0; i < retVal.size(); i++) {
IBase next = retVal.get(i);
/*
* If we have automatically contained any resources via
* their references, this ensures that we output the new
* local reference
*/
if (next instanceof IBaseReference) {
IBaseReference nextRef = (IBaseReference) next;
String refText = determineReferenceText(nextRef, theCompositeChildElement, theResource);
if (!StringUtils.equals(refText, nextRef.getReferenceElement().getValue())) {
if (retVal == theValues) {
retVal = new ArrayList<>(theValues);
}
IBaseReference newRef = (IBaseReference)
myContext.getElementDefinition(nextRef.getClass()).newInstance();
myContext.newTerser().cloneInto(nextRef, newRef, true);
newRef.setReference(refText);
retVal.set(i, newRef);
}
}
}
return retVal;
}
private String getSubsettedCodeSystem() {
if (myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
return Constants.TAG_SUBSETTED_SYSTEM_R4;
} else {
return Constants.TAG_SUBSETTED_SYSTEM_DSTU3;
}
}
@Override
public IParser setDontStripVersionsFromReferencesAtPaths(String... thePaths) {
if (thePaths == null) {
setDontStripVersionsFromReferencesAtPaths((List) null);
} else {
setDontStripVersionsFromReferencesAtPaths(Arrays.asList(thePaths));
}
return this;
}
@SuppressWarnings("unchecked")
@Override
public IParser setDontStripVersionsFromReferencesAtPaths(Collection thePaths) {
if (thePaths == null) {
myDontStripVersionsFromReferencesAtPaths = Collections.emptySet();
} else if (thePaths instanceof HashSet) {
myDontStripVersionsFromReferencesAtPaths = (Set) ((HashSet) thePaths).clone();
} else {
myDontStripVersionsFromReferencesAtPaths = new HashSet<>(thePaths);
}
return this;
}
@Override
public IParser setOmitResourceId(boolean theOmitResourceId) {
myOmitResourceId = theOmitResourceId;
return this;
}
@Override
public IParser setOverrideResourceIdWithBundleEntryFullUrl(Boolean theOverrideResourceIdWithBundleEntryFullUrl) {
myOverrideResourceIdWithBundleEntryFullUrl = theOverrideResourceIdWithBundleEntryFullUrl;
return this;
}
@Override
public IParser setParserErrorHandler(IParserErrorHandler theErrorHandler) {
Validate.notNull(theErrorHandler, "theErrorHandler must not be null");
myErrorHandler = theErrorHandler;
return this;
}
@Override
public IParser setServerBaseUrl(String theUrl) {
myServerBaseUrl = isNotBlank(theUrl) ? theUrl : null;
return this;
}
@Override
public IParser setStripVersionsFromReferences(Boolean theStripVersionsFromReferences) {
myStripVersionsFromReferences = theStripVersionsFromReferences;
return this;
}
@Override
public IParser setSummaryMode(boolean theSummaryMode) {
mySummaryMode = theSummaryMode;
return this;
}
@Override
public IParser setSuppressNarratives(boolean theSuppressNarratives) {
mySuppressNarratives = theSuppressNarratives;
return this;
}
protected boolean shouldAddSubsettedTag(EncodeContext theEncodeContext) {
if (isSummaryMode()) {
return true;
}
if (isSuppressNarratives()) {
return true;
}
if (myEncodeElements != null) {
if (isEncodeElementsAppliesToChildResourcesOnly()
&& theEncodeContext.getResourcePath().size() < 2) {
return false;
}
String currentResourceName = theEncodeContext
.getResourcePath()
.get(theEncodeContext.getResourcePath().size() - 1)
.getName();
return myEncodeElementsAppliesToResourceTypes == null
|| myEncodeElementsAppliesToResourceTypes.contains(currentResourceName);
}
return false;
}
protected boolean shouldEncodeResourceId(IBaseResource theResource, EncodeContext theEncodeContext) {
boolean retVal = true;
if (isOmitResourceId() && theEncodeContext.getPath().size() == 1) {
retVal = false;
} else {
if (myDontEncodeElements != null) {
String resourceName = myContext.getResourceType(theResource);
if (myDontEncodeElements.stream().anyMatch(t -> t.equalsPath(resourceName + ".id"))) {
retVal = false;
} else if (myDontEncodeElements.stream().anyMatch(t -> t.equalsPath("*.id"))) {
retVal = false;
} else if (theEncodeContext.getResourcePath().size() == 1
&& myDontEncodeElements.stream().anyMatch(t -> t.equalsPath("id"))) {
retVal = false;
}
}
}
return retVal;
}
/**
* Used for DSTU2 only
*/
protected boolean shouldEncodeResourceMeta(IResource theResource) {
return shouldEncodePath(theResource, "meta");
}
/**
* Used for DSTU2 only
*/
protected boolean shouldEncodePath(IResource theResource, String thePath) {
if (myDontEncodeElements != null) {
String resourceName = myContext.getResourceType(theResource);
if (myDontEncodeElements.stream().anyMatch(t -> t.equalsPath(resourceName + "." + thePath))) {
return false;
} else return myDontEncodeElements.stream().noneMatch(t -> t.equalsPath("*." + thePath));
}
return true;
}
private String subsetDescription() {
return "Resource encoded in summary mode";
}
protected void throwExceptionForUnknownChildType(
BaseRuntimeChildDefinition nextChild, Class theType) {
if (nextChild instanceof BaseRuntimeDeclaredChildDefinition) {
StringBuilder b = new StringBuilder();
b.append(nextChild.getElementName());
b.append(" has type ");
b.append(theType.getName());
b.append(" but this is not a valid type for this element");
if (nextChild instanceof RuntimeChildChoiceDefinition) {
RuntimeChildChoiceDefinition choice = (RuntimeChildChoiceDefinition) nextChild;
b.append(" - Expected one of: " + choice.getValidChildTypes());
}
throw new DataFormatException(Msg.code(1831) + b);
}
throw new DataFormatException(Msg.code(1832) + nextChild + " has no child of type " + theType);
}
protected boolean shouldEncodeResource(String theName) {
if (myDontEncodeElements != null) {
for (EncodeContextPath next : myDontEncodeElements) {
if (next.equalsPath(theName)) {
return false;
}
}
}
return true;
}
protected boolean isFhirVersionLessThanOrEqualTo(FhirVersionEnum theFhirVersionEnum) {
final FhirVersionEnum apiFhirVersion = myContext.getVersion().getVersion();
return theFhirVersionEnum == apiFhirVersion || apiFhirVersion.isOlderThan(theFhirVersionEnum);
}
protected void containResourcesInReferences(IBaseResource theResource) {
/*
* If a UUID is present in Bundle.entry.fullUrl but no value is present
* in Bundle.entry.resource.id, the resource has a discrete identity which
* should be copied into the resource ID. It will not be serialized in
* Resource.id because it's a placeholder/UUID value, but its presence there
* informs the serializer that we don't need to contain this resource.
*/
if (theResource instanceof IBaseBundle) {
List> entries =
BundleUtil.getBundleEntryFullUrlsAndResources(getContext(), (IBaseBundle) theResource);
for (Pair nextEntry : entries) {
String fullUrl = nextEntry.getKey();
IBaseResource resource = nextEntry.getValue();
if (startsWith(fullUrl, "urn:")) {
if (resource != null && resource.getIdElement().getValue() == null) {
resource.getIdElement().setValue(fullUrl);
}
}
}
}
myContainedResources = getContext().newTerser().containResources(theResource);
}
class ChildNameAndDef {
private final BaseRuntimeElementDefinition myChildDef;
private final String myChildName;
public ChildNameAndDef(String theChildName, BaseRuntimeElementDefinition theChildDef) {
myChildName = theChildName;
myChildDef = theChildDef;
}
public BaseRuntimeElementDefinition getChildDef() {
return myChildDef;
}
public String getChildName() {
return myChildName;
}
}
/**
* EncodeContext is a shared state object that is passed around the
* encode process
*/
public class EncodeContext extends EncodeContextPath {
private final Map> myCompositeChildrenCache = new HashMap<>();
public Map> getCompositeChildrenCache() {
return myCompositeChildrenCache;
}
}
protected class CompositeChildElement {
private final BaseRuntimeChildDefinition myDef;
private final CompositeChildElement myParent;
private final RuntimeResourceDefinition myResDef;
private final EncodeContext myEncodeContext;
public CompositeChildElement(
CompositeChildElement theParent,
@Nullable BaseRuntimeChildDefinition theDef,
EncodeContext theEncodeContext) {
myDef = theDef;
myParent = theParent;
myResDef = null;
myEncodeContext = theEncodeContext;
if (ourLog.isTraceEnabled()) {
if (theParent != null) {
StringBuilder path = theParent.buildPath();
if (path != null) {
path.append('.');
if (myDef != null) {
path.append(myDef.getElementName());
}
ourLog.trace(" * Next path: {}", path);
}
}
}
}
public CompositeChildElement(RuntimeResourceDefinition theResDef, EncodeContext theEncodeContext) {
myResDef = theResDef;
myDef = null;
myParent = null;
myEncodeContext = theEncodeContext;
}
@Override
public String toString() {
return myDef.getElementName();
}
private void addParent(CompositeChildElement theParent, StringBuilder theB) {
if (theParent != null) {
if (theParent.myResDef != null) {
theB.append(theParent.myResDef.getName());
return;
}
if (theParent.myParent != null) {
addParent(theParent.myParent, theB);
}
if (theParent.myDef != null) {
if (theB.length() > 0) {
theB.append('.');
}
theB.append(theParent.myDef.getElementName());
}
}
}
public boolean anyPathMatches(Set thePaths) {
StringBuilder b = new StringBuilder();
addParent(this, b);
String path = b.toString();
return thePaths.contains(path);
}
private StringBuilder buildPath() {
if (myResDef != null) {
StringBuilder b = new StringBuilder();
b.append(myResDef.getName());
return b;
} else if (myParent != null) {
StringBuilder b = myParent.buildPath();
if (b != null && myDef != null) {
b.append('.');
b.append(myDef.getElementName());
}
return b;
} else {
return null;
}
}
private boolean checkIfParentShouldBeEncodedAndBuildPath() {
List encodeElements = myEncodeElements;
String currentResourceName = myEncodeContext
.getResourcePath()
.get(myEncodeContext.getResourcePath().size() - 1)
.getName();
if (myEncodeElementsAppliesToResourceTypes != null
&& !myEncodeElementsAppliesToResourceTypes.contains(currentResourceName)) {
encodeElements = null;
}
boolean retVal = checkIfPathMatchesForEncoding(encodeElements, true);
/*
* We force the meta tag to be encoded even if it's not specified as an element in the
* elements filter, specifically because we'll need it in order to automatically add
* the SUBSETTED tag
*/
if (!retVal) {
if ("meta".equals(myEncodeContext.getLeafResourcePathFirstField())
&& shouldAddSubsettedTag(myEncodeContext)) {
// The next element is a child of the element
retVal = true;
} else if ("meta".equals(myDef.getElementName()) && shouldAddSubsettedTag(myEncodeContext)) {
// The next element is the element
retVal = true;
}
}
return retVal;
}
private boolean checkIfParentShouldNotBeEncodedAndBuildPath() {
return checkIfPathMatchesForEncoding(myDontEncodeElements, false);
}
private boolean checkIfPathMatchesForEncoding(
List theElements, boolean theCheckingForEncodeElements) {
boolean retVal = false;
if (myDef != null) {
myEncodeContext.pushPath(myDef.getElementName(), false);
}
if (theCheckingForEncodeElements
&& isEncodeElementsAppliesToChildResourcesOnly()
&& myEncodeContext.getResourcePath().size() < 2) {
retVal = true;
} else if (theElements == null) {
retVal = true;
} else {
EncodeContextPath currentResourcePath = myEncodeContext.getCurrentResourcePath();
ourLog.trace("Current resource path: {}", currentResourcePath);
for (EncodeContextPath next : theElements) {
if (next.startsWith(currentResourcePath, true)) {
if (theCheckingForEncodeElements
|| next.getPath().size()
== currentResourcePath.getPath().size()) {
retVal = true;
break;
}
}
if (next.getPath().get(next.getPath().size() - 1).getName().equals("(mandatory)")) {
if (myDef.getMin() > 0) {
retVal = true;
break;
}
if (currentResourcePath.getPath().size()
> next.getPath().size()) {
retVal = true;
break;
}
}
}
}
if (myDef != null) {
myEncodeContext.popPath();
}
return retVal;
}
public BaseRuntimeChildDefinition getDef() {
return myDef;
}
public CompositeChildElement getParent() {
return myParent;
}
public boolean shouldBeEncoded(boolean theContainedResource) {
boolean retVal = true;
if (myEncodeElements != null) {
retVal = checkIfParentShouldBeEncodedAndBuildPath();
}
if (retVal && myDontEncodeElements != null) {
retVal = !checkIfParentShouldNotBeEncodedAndBuildPath();
}
if (theContainedResource) {
retVal = !notEncodeForContainedResource.contains(myDef.getElementName());
}
if (retVal && isSummaryMode() && (getDef() == null || !getDef().isSummary())) {
String resourceName = myEncodeContext.getLeafResourceName();
// Technically the spec says we shouldn't include extensions in CapabilityStatement
// but we will do so because there are people who depend on this behaviour, at least
// as of 2019-07. See
// https://github.com/smart-on-fhir/Swift-FHIR/issues/26
// for example.
if (("Conformance".equals(resourceName) || "CapabilityStatement".equals(resourceName))
&& ("extension".equals(myDef.getElementName())
|| "extension".equals(myEncodeContext.getLeafElementName()))) {
// skip
} else {
retVal = false;
}
}
return retVal;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((myDef == null) ? 0 : myDef.hashCode());
result = prime * result + ((myParent == null) ? 0 : myParent.hashCode());
result = prime * result + ((myResDef == null) ? 0 : myResDef.hashCode());
result = prime * result + ((myEncodeContext == null) ? 0 : myEncodeContext.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj instanceof CompositeChildElement) {
final CompositeChildElement that = (CompositeChildElement) obj;
return Objects.equals(this.getEnclosingInstance(), that.getEnclosingInstance())
&& Objects.equals(this.myDef, that.myDef)
&& Objects.equals(this.myParent, that.myParent)
&& Objects.equals(this.myResDef, that.myResDef)
&& Objects.equals(this.myEncodeContext, that.myEncodeContext);
}
return false;
}
private BaseParser getEnclosingInstance() {
return BaseParser.this;
}
}
private static class Key {
private final BaseRuntimeElementCompositeDefinition resDef;
private final boolean theContainedResource;
private final BaseParser.CompositeChildElement theParent;
private final BaseParser.EncodeContext theEncodeContext;
public Key(
BaseRuntimeElementCompositeDefinition resDef,
final boolean theContainedResource,
final BaseParser.CompositeChildElement theParent,
BaseParser.EncodeContext theEncodeContext) {
this.resDef = resDef;
this.theContainedResource = theContainedResource;
this.theParent = theParent;
this.theEncodeContext = theEncodeContext;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((resDef == null) ? 0 : resDef.hashCode());
result = prime * result + (theContainedResource ? 1231 : 1237);
result = prime * result + ((theParent == null) ? 0 : theParent.hashCode());
result = prime * result + ((theEncodeContext == null) ? 0 : theEncodeContext.hashCode());
return result;
}
@Override
public boolean equals(final Object obj) {
if (this == obj) {
return true;
}
if (obj instanceof Key) {
final Key that = (Key) obj;
return Objects.equals(this.resDef, that.resDef)
&& this.theContainedResource == that.theContainedResource
&& Objects.equals(this.theParent, that.theParent)
&& Objects.equals(this.theEncodeContext, that.theEncodeContext);
}
return false;
}
}
protected static List extractMetadataListNotNull(IResource resource, ResourceMetadataKeyEnum> key) {
List securityLabels = key.get(resource);
if (securityLabels == null) {
securityLabels = Collections.emptyList();
}
return new ArrayList<>(securityLabels);
}
static boolean hasNoExtensions(IBase theElement) {
if (theElement instanceof ISupportsUndeclaredExtensions) {
ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) theElement;
if (res.getUndeclaredExtensions().size() > 0
|| res.getUndeclaredModifierExtensions().size() > 0) {
return false;
}
}
if (theElement instanceof IBaseHasExtensions) {
IBaseHasExtensions res = (IBaseHasExtensions) theElement;
if (res.hasExtension()) {
return false;
}
}
if (theElement instanceof IBaseHasModifierExtensions) {
IBaseHasModifierExtensions res = (IBaseHasModifierExtensions) theElement;
return !res.hasModifierExtension();
}
return true;
}
}
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