package ca.uhn.fhir.parser;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* 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%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.IOException;
import java.io.Reader;
import java.io.StringReader;
import java.io.StringWriter;
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.IdentityHashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
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.IDomainResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
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.model.api.Bundle;
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.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.UrlUtil;
public abstract class BaseParser implements IParser {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
private ContainedResources myContainedResources;
private FhirContext myContext;
private Set<String> myDontEncodeElements;
private boolean myDontEncodeElementsIncludesStars;
private Set<String> myEncodeElements;
private Set<String> myEncodeElementsAppliesToResourceTypes;
private boolean myEncodeElementsIncludesStars;
private IIdType myEncodeForceResourceId;
private IParserErrorHandler myErrorHandler;
private boolean myOmitResourceId;
private List<Class<? extends IBaseResource>> myPreferTypes;
private String myServerBaseUrl;
private Boolean myStripVersionsFromReferences;
private Boolean myOverrideResourceIdWithBundleEntryFullUrl;
private boolean mySummaryMode;
private boolean mySuppressNarratives;
private Set<String> myDontStripVersionsFromReferencesAtPaths;
/**
* Constructor
*
* @param theParserErrorHandler
*/
public BaseParser(FhirContext theContext, IParserErrorHandler theParserErrorHandler) {
myContext = theContext;
myErrorHandler = theParserErrorHandler;
}
protected Iterable<CompositeChildElement> compositeChildIterator(IBase theCompositeElement, final boolean theContainedResource, final CompositeChildElement theParent) {
BaseRuntimeElementCompositeDefinition<?> elementDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theCompositeElement.getClass());
final List<BaseRuntimeChildDefinition> children = elementDef.getChildrenAndExtension();
return new Iterable<BaseParser.CompositeChildElement>() {
@Override
public Iterator<CompositeChildElement> iterator() {
return new Iterator<CompositeChildElement>() {
private Iterator<? extends BaseRuntimeChildDefinition> myChildrenIter;
private Boolean myHasNext = null;
private CompositeChildElement myNext;
/**
* Constructor
*/
{
myChildrenIter = children.iterator();
}
@Override
public boolean hasNext() {
if (myHasNext != null) {
return myHasNext;
}
myNext = null;
do {
if (myChildrenIter.hasNext() == false) {
myHasNext = Boolean.FALSE;
return false;
}
myNext = new CompositeChildElement(theParent, myChildrenIter.next());
/*
* There are lots of reasons we might skip encoding a particular child
*/
if (myNext.getDef().getElementName().equals("id")) {
myNext = null;
} else if (!myNext.shouldBeEncoded()) {
myNext = null;
} else if (isSummaryMode() && !myNext.getDef().isSummary()) {
myNext = null;
} else if (myNext.getDef() instanceof RuntimeChildNarrativeDefinition) {
if (isSuppressNarratives() || isSummaryMode()) {
myNext = null;
} else if (theContainedResource) {
myNext = null;
}
} else if (myNext.getDef() instanceof RuntimeChildContainedResources) {
if (theContainedResource) {
myNext = null;
}
}
} while (myNext == null);
myHasNext = true;
return true;
}
@Override
public CompositeChildElement next() {
if (myHasNext == null) {
if (!hasNext()) {
throw new IllegalStateException();
}
}
CompositeChildElement retVal = myNext;
myNext = null;
myHasNext = null;
return retVal;
}
@Override
public void remove() {
throw new UnsupportedOperationException();
}
};
}
};
}
private void containResourcesForEncoding(ContainedResources theContained, IBaseResource theResource, IBaseResource theTarget) {
Set<String> allIds = new HashSet<String>();
Map<String, IBaseResource> existingIdToContainedResource = null;
if (theTarget instanceof IResource) {
List<? extends IResource> containedResources = ((IResource) theTarget).getContained().getContainedResources();
for (IResource next : containedResources) {
String nextId = next.getId().getValue();
if (StringUtils.isNotBlank(nextId)) {
if (!nextId.startsWith("#")) {
nextId = '#' + nextId;
}
allIds.add(nextId);
if (existingIdToContainedResource == null) {
existingIdToContainedResource = new HashMap<String, IBaseResource>();
}
existingIdToContainedResource.put(nextId, next);
}
}
} else if (theTarget instanceof IDomainResource) {
List<? extends IAnyResource> containedResources = ((IDomainResource) theTarget).getContained();
for (IAnyResource next : containedResources) {
String nextId = next.getIdElement().getValue();
if (StringUtils.isNotBlank(nextId)) {
if (!nextId.startsWith("#")) {
nextId = '#' + nextId;
}
allIds.add(nextId);
if (existingIdToContainedResource == null) {
existingIdToContainedResource = new HashMap<String, IBaseResource>();
}
existingIdToContainedResource.put(nextId, next);
}
}
} else {
// no resources to contain
}
{
List<IBaseReference> allElements = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
for (IBaseReference next : allElements) {
IBaseResource resource = next.getResource();
if (resource != null) {
if (resource.getIdElement().isEmpty() || resource.getIdElement().isLocal()) {
if (theContained.getResourceId(resource) != null) {
// Prevent infinite recursion if there are circular loops in the contained resources
continue;
}
theContained.addContained(resource);
if (resource.getIdElement().isLocal() && existingIdToContainedResource != null) {
existingIdToContainedResource.remove(resource.getIdElement().getValue());
}
} else {
continue;
}
containResourcesForEncoding(theContained, resource, theTarget);
} else if (next.getReferenceElement().isLocal()) {
if (existingIdToContainedResource != null) {
IBaseResource potentialTarget = existingIdToContainedResource.remove(next.getReferenceElement().getValue());
if (potentialTarget != null) {
theContained.addContained(next.getReferenceElement(), potentialTarget);
containResourcesForEncoding(theContained, potentialTarget, theTarget);
}
}
}
}
}
}
protected void containResourcesForEncoding(IBaseResource theResource) {
ContainedResources contained = new ContainedResources();
containResourcesForEncoding(contained, theResource, theResource);
myContainedResources = contained;
}
private String determineReferenceText(IBaseReference theRef, CompositeChildElement theCompositeChildElement) {
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)) {
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)) {
return ref.toUnqualifiedVersionless().getValue();
}
return ref.toUnqualified().getValue();
}
if (isStripVersionsFromReferences(theCompositeChildElement)) {
return ref.toVersionless().getValue();
}
return ref.getValue();
}
private boolean isStripVersionsFromReferences(CompositeChildElement theCompositeChildElement) {
Boolean stripVersionsFromReferences = myStripVersionsFromReferences;
if (stripVersionsFromReferences != null) {
return stripVersionsFromReferences;
}
if (myContext.getParserOptions().isStripVersionsFromReferences() == false) {
return false;
}
Set<String> dontStripVersionsFromReferencesAtPaths = myDontStripVersionsFromReferencesAtPaths;
if (dontStripVersionsFromReferencesAtPaths != null) {
if (dontStripVersionsFromReferencesAtPaths.isEmpty() == false && theCompositeChildElement.anyPathMatches(dontStripVersionsFromReferencesAtPaths)) {
return false;
}
}
dontStripVersionsFromReferencesAtPaths = myContext.getParserOptions().getDontStripVersionsFromReferencesAtPaths();
if (dontStripVersionsFromReferencesAtPaths.isEmpty() == false && theCompositeChildElement.anyPathMatches(dontStripVersionsFromReferencesAtPaths)) {
return false;
}
return true;
}
private boolean isOverrideResourceIdWithBundleEntryFullUrl() {
Boolean overrideResourceIdWithBundleEntryFullUrl = myOverrideResourceIdWithBundleEntryFullUrl;
if (overrideResourceIdWithBundleEntryFullUrl != null) {
return overrideResourceIdWithBundleEntryFullUrl;
}
return myContext.getParserOptions().isOverrideResourceIdWithBundleEntryFullUrl();
}
protected abstract void doEncodeBundleToWriter(Bundle theBundle, Writer theWriter) throws IOException, DataFormatException;
protected abstract void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException, DataFormatException;
protected abstract <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) throws DataFormatException;
@Override
public String encodeBundleToString(Bundle theBundle) throws DataFormatException {
if (theBundle == null) {
throw new NullPointerException("Bundle can not be null");
}
StringWriter stringWriter = new StringWriter();
try {
encodeBundleToWriter(theBundle, stringWriter);
} catch (IOException e) {
throw new Error("Encountered IOException during write to string - This should not happen!");
}
return stringWriter.toString();
}
@Override
public final void encodeBundleToWriter(Bundle theBundle, Writer theWriter) throws IOException, DataFormatException {
Validate.notNull(theBundle, "theBundle must not be null");
Validate.notNull(theWriter, "theWriter must not be null");
doEncodeBundleToWriter(theBundle, theWriter);
}
@Override
public String encodeResourceToString(IBaseResource theResource) throws DataFormatException {
Writer stringWriter = new StringWriter();
try {
encodeResourceToWriter(theResource, stringWriter);
} catch (IOException e) {
throw new Error("Encountered IOException during write to string - This should not happen!");
}
return stringWriter.toString();
}
@Override
public final void encodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException, DataFormatException {
Validate.notNull(theResource, "theResource can not be null");
Validate.notNull(theWriter, "theWriter can not be null");
if (theResource.getStructureFhirVersionEnum() != myContext.getVersion().getVersion()) {
throw new IllegalArgumentException(
"This parser is for FHIR version " + myContext.getVersion().getVersion() + " - Can not encode a structure for version " + theResource.getStructureFhirVersionEnum());
}
doEncodeResourceToWriter(theResource, theWriter);
}
@Override
public String encodeTagListToString(TagList theTagList) {
Writer stringWriter = new StringWriter();
try {
encodeTagListToWriter(theTagList, stringWriter);
} catch (IOException e) {
throw new Error("Encountered IOException during write to string - This should not happen!");
}
return stringWriter.toString();
}
private void filterCodingsWithNoCodeOrSystem(List<? extends IBaseCoding> 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<? extends IBase> 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<? extends IBase> 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<? extends IBase>) nextSuperType);
Class<?> nextChildType = def.getImplementingClass();
childDef = theChild.getChildElementDefinitionByDatatype((Class<? extends IBase>) nextChildType);
childName = theChild.getChildNameByDatatype((Class<? extends IBase>) 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;
}
ContainedResources getContainedResources() {
return myContainedResources;
}
/**
* See {@link #setEncodeElements(Set)}
*/
@Override
public Set<String> getEncodeElements() {
return myEncodeElements;
}
/**
* See {@link #setEncodeElementsAppliesToResourceTypes(Set)}
*/
@Override
public Set<String> getEncodeElementsAppliesToResourceTypes() {
return myEncodeElementsAppliesToResourceTypes;
}
@Override
public IIdType getEncodeForceResourceId() {
return myEncodeForceResourceId;
}
protected IParserErrorHandler getErrorHandler() {
return myErrorHandler;
}
protected TagList getMetaTagsForEncoding(IResource theIResource) {
TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(theIResource);
if (shouldAddSubsettedTag()) {
tags = new TagList(tags);
tags.add(new Tag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE, subsetDescription()));
}
return tags;
}
@Override
public List<Class<? extends IBaseResource>> getPreferTypes() {
return myPreferTypes;
}
@SuppressWarnings("deprecation")
protected <T extends IPrimitiveType<String>> List<T> getProfileTagsForEncoding(IBaseResource theResource, List<T> 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;
}
if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
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<T> newList = new ArrayList<T>();
newList.addAll(theProfiles);
BaseRuntimeElementDefinition<?> idElement = myContext.getElementDefinition("id");
@SuppressWarnings("unchecked")
T newId = (T) idElement.newInstance();
newId.setValue(profile);
newList.add(newId);
return newList;
}
}
return theProfiles;
}
/**
* If set to <code>true</code> (default is <code>false</code>), 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 isOmitResourceId() {
return myOmitResourceId;
}
@Override
public Boolean getStripVersionsFromReferences() {
return myStripVersionsFromReferences;
}
@Override
public Boolean getOverrideResourceIdWithBundleEntryFullUrl() {
return myOverrideResourceIdWithBundleEntryFullUrl;
}
@Override
public boolean isSummaryMode() {
return mySummaryMode;
}
/**
* If set to <code>true</code> (default is <code>false</code>), narratives will not be included in the encoded
* values.
*
* @since 1.2
*/
public boolean isSuppressNarratives() {
return mySuppressNarratives;
}
@Override
public Bundle parseBundle(Reader theReader) {
if (myContext.getVersion().getVersion() == FhirVersionEnum.DSTU2_HL7ORG) {
throw new IllegalStateException("Can't parse DSTU1 (Atom) bundle in HL7.org DSTU2 mode. Use parseResource(Bundle.class, foo) instead.");
}
return parseBundle(null, theReader);
}
@Override
public Bundle parseBundle(String theXml) throws ConfigurationException, DataFormatException {
StringReader reader = new StringReader(theXml);
return parseBundle(reader);
}
@Override
public <T extends IBaseResource> T parseResource(Class<T> 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())) {
BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
BaseRuntimeElementCompositeDefinition<?> entryDef = (BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
List<IBase> entries = entryChild.getAccessor().getValues(retVal);
if (entries != null) {
for (IBase nextEntry : entries) {
/**
* If Bundle.entry.fullUrl is populated, set the resource ID to that
*/
// TODO: should emit a warning and maybe notify the error handler if the resource ID doesn't match the
// fullUrl idPart
BaseRuntimeChildDefinition fullUrlChild = entryDef.getChildByName("fullUrl");
if (fullUrlChild == null) {
continue; // TODO: remove this once the data model in tinder plugin catches up to 1.2
}
if (isOverrideResourceIdWithBundleEntryFullUrl()) {
List<IBase> fullUrl = fullUrlChild.getAccessor().getValues(nextEntry);
if (fullUrl != null && !fullUrl.isEmpty()) {
IPrimitiveType<?> value = (IPrimitiveType<?>) fullUrl.get(0);
if (value.isEmpty() == false) {
List<IBase> entryResources = entryDef.getChildByName("resource").getAccessor().getValues(nextEntry);
if (entryResources != null && entryResources.size() > 0) {
IBaseResource res = (IBaseResource) entryResources.get(0);
String versionId = res.getIdElement().getVersionIdPart();
res.setId(value.getValueAsString());
if (isNotBlank(versionId) && res.getIdElement().hasVersionIdPart() == false) {
res.setId(res.getIdElement().withVersion(versionId));
}
}
}
}
}
}
}
}
return retVal;
}
@SuppressWarnings("cast")
@Override
public <T extends IBaseResource> T parseResource(Class<T> theResourceType, String theMessageString) {
StringReader reader = new StringReader(theMessageString);
return (T) 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);
}
@Override
public TagList parseTagList(String theString) {
return parseTagList(new StringReader(theString));
}
protected List<? extends IBase> preProcessValues(BaseRuntimeChildDefinition theMetaChildUncast, IBaseResource theResource, List<? extends IBase> theValues,
CompositeChildElement theCompositeChildElement) {
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("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<? extends IPrimitiveType<String>> newProfileList = getProfileTagsForEncoding(theResource, metaValue.getProfile());
List<? extends IPrimitiveType<String>> oldProfileList = metaValue.getProfile();
if (oldProfileList != newProfileList) {
oldProfileList.clear();
for (IPrimitiveType<String> next : newProfileList) {
if (isNotBlank(next.getValue())) {
metaValue.addProfile(next.getValue());
}
}
}
if (shouldAddSubsettedTag()) {
IBaseCoding coding = metaValue.addTag();
coding.setCode(Constants.TAG_SUBSETTED_CODE);
coding.setSystem(Constants.TAG_SUBSETTED_SYSTEM);
coding.setDisplay(subsetDescription());
}
return Collections.singletonList(metaValue);
}
}
@SuppressWarnings("unchecked")
List<IBase> retVal = (List<IBase>) 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);
if (!StringUtils.equals(refText, nextRef.getReferenceElement().getValue())) {
if (retVal == theValues) {
retVal = new ArrayList<IBase>(theValues);
}
IBaseReference newRef = (IBaseReference) myContext.getElementDefinition(nextRef.getClass()).newInstance();
myContext.newTerser().cloneInto(nextRef, newRef, true);
newRef.setReference(refText);
retVal.set(i, newRef);
}
}
}
return retVal;
}
@Override
public void setDontEncodeElements(Set<String> theDontEncodeElements) {
myDontEncodeElementsIncludesStars = false;
if (theDontEncodeElements == null || theDontEncodeElements.isEmpty()) {
myDontEncodeElements = null;
} else {
myDontEncodeElements = theDontEncodeElements;
for (String next : theDontEncodeElements) {
if (next.startsWith("*.")) {
myDontEncodeElementsIncludesStars = true;
}
}
}
}
@Override
public void setEncodeElements(Set<String> theEncodeElements) {
myEncodeElementsIncludesStars = false;
if (theEncodeElements == null || theEncodeElements.isEmpty()) {
myEncodeElements = null;
} else {
myEncodeElements = theEncodeElements;
for (String next : theEncodeElements) {
if (next.startsWith("*.")) {
myEncodeElementsIncludesStars = true;
}
}
}
}
@Override
public void setEncodeElementsAppliesToResourceTypes(Set<String> theEncodeElementsAppliesToResourceTypes) {
if (theEncodeElementsAppliesToResourceTypes == null || theEncodeElementsAppliesToResourceTypes.isEmpty()) {
myEncodeElementsAppliesToResourceTypes = null;
} else {
myEncodeElementsAppliesToResourceTypes = theEncodeElementsAppliesToResourceTypes;
}
}
@Override
public BaseParser setEncodeForceResourceId(IIdType theEncodeForceResourceId) {
myEncodeForceResourceId = theEncodeForceResourceId;
return this;
}
@Override
public IParser setOmitResourceId(boolean theOmitResourceId) {
myOmitResourceId = theOmitResourceId;
return this;
}
@Override
public IParser setParserErrorHandler(IParserErrorHandler theErrorHandler) {
Validate.notNull(theErrorHandler, "theErrorHandler must not be null");
myErrorHandler = theErrorHandler;
return this;
}
@Override
public void setPreferTypes(List<Class<? extends IBaseResource>> thePreferTypes) {
if (thePreferTypes != null) {
ArrayList<Class<? extends IBaseResource>> types = new ArrayList<Class<? extends IBaseResource>>();
for (Class<? extends IBaseResource> next : thePreferTypes) {
if (Modifier.isAbstract(next.getModifiers()) == false) {
types.add(next);
}
}
myPreferTypes = Collections.unmodifiableList(types);
} else {
myPreferTypes = thePreferTypes;
}
}
@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 setOverrideResourceIdWithBundleEntryFullUrl(Boolean theOverrideResourceIdWithBundleEntryFullUrl) {
myOverrideResourceIdWithBundleEntryFullUrl = theOverrideResourceIdWithBundleEntryFullUrl;
return this;
}
@Override
public IParser setDontStripVersionsFromReferencesAtPaths(String... thePaths) {
if (thePaths == null) {
setDontStripVersionsFromReferencesAtPaths((List<String>) null);
} else {
setDontStripVersionsFromReferencesAtPaths(Arrays.asList(thePaths));
}
return this;
}
@SuppressWarnings("unchecked")
@Override
public IParser setDontStripVersionsFromReferencesAtPaths(Collection<String> thePaths) {
if (thePaths == null) {
myDontStripVersionsFromReferencesAtPaths = Collections.emptySet();
} else if (thePaths instanceof HashSet) {
myDontStripVersionsFromReferencesAtPaths = (Set<String>) ((HashSet<String>) thePaths).clone();
} else {
myDontStripVersionsFromReferencesAtPaths = new HashSet<String>(thePaths);
}
return this;
}
@Override
public Set<String> getDontStripVersionsFromReferencesAtPaths() {
return myDontStripVersionsFromReferencesAtPaths;
}
@Override
public IParser setSummaryMode(boolean theSummaryMode) {
mySummaryMode = theSummaryMode;
return this;
}
@Override
public IParser setSuppressNarratives(boolean theSuppressNarratives) {
mySuppressNarratives = theSuppressNarratives;
return this;
}
protected boolean shouldAddSubsettedTag() {
return isSummaryMode() || isSuppressNarratives() || getEncodeElements() != null;
}
protected boolean shouldEncodeResourceId(IBaseResource theResource) {
boolean retVal = true;
if (isOmitResourceId()) {
retVal = false;
} else {
if (myDontEncodeElements != null) {
String resourceName = myContext.getResourceDefinition(theResource).getName();
if (myDontEncodeElements.contains(resourceName + ".id")) {
retVal = false;
} else if (myDontEncodeElements.contains("*.id")) {
retVal = false;
}
}
}
return retVal;
}
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 String getServerBaseUrl() {
return myServerBaseUrl;
}
/**
* Used for DSTU2 only
*/
protected boolean shouldEncodeResourceMeta(IResource theResource) {
if (myDontEncodeElements != null) {
String resourceName = myContext.getResourceDefinition(theResource).getName();
if (myDontEncodeElements.contains(resourceName + ".meta")) {
return false;
} else if (myDontEncodeElements.contains("*.meta")) {
return false;
}
}
return true;
}
private String subsetDescription() {
return "Resource encoded in summary mode";
}
protected void throwExceptionForUnknownChildType(BaseRuntimeChildDefinition nextChild, Class<? extends IBase> theType) {
if (nextChild instanceof BaseRuntimeDeclaredChildDefinition) {
StringBuilder b = new StringBuilder();
b.append(((BaseRuntimeDeclaredChildDefinition) 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(b.toString());
}
throw new DataFormatException(nextChild + " has no child of type " + theType);
}
protected static <T> List<T> extractMetadataListNotNull(IResource resource, ResourceMetadataKeyEnum<List<T>> key) {
List<? extends T> securityLabels = key.get(resource);
if (securityLabels == null) {
securityLabels = Collections.emptyList();
}
return new ArrayList<T>(securityLabels);
}
static boolean hasExtensions(IBase theElement) {
if (theElement instanceof ISupportsUndeclaredExtensions) {
ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) theElement;
if (res.getUndeclaredExtensions().size() > 0 || res.getUndeclaredModifierExtensions().size() > 0) {
return true;
}
}
if (theElement instanceof IBaseHasExtensions) {
IBaseHasExtensions res = (IBaseHasExtensions) theElement;
if (res.hasExtension()) {
return true;
}
}
if (theElement instanceof IBaseHasModifierExtensions) {
IBaseHasModifierExtensions res = (IBaseHasModifierExtensions) theElement;
if (res.hasModifierExtension()) {
return true;
}
}
return false;
}
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;
}
}
protected class CompositeChildElement {
private final BaseRuntimeChildDefinition myDef;
private final CompositeChildElement myParent;
private final RuntimeResourceDefinition myResDef;
public CompositeChildElement(CompositeChildElement theParent, BaseRuntimeChildDefinition theDef) {
myDef = theDef;
myParent = theParent;
myResDef = null;
if (ourLog.isTraceEnabled()) {
if (theParent != null) {
StringBuilder path = theParent.buildPath();
if (path != null) {
path.append('.');
path.append(myDef.getElementName());
ourLog.trace(" * Next path: {}", path.toString());
}
}
}
}
public boolean anyPathMatches(Set<String> thePaths) {
StringBuilder b = new StringBuilder();
addParent(this, b);
String path = b.toString();
return thePaths.contains(path);
}
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 CompositeChildElement(RuntimeResourceDefinition theResDef) {
myResDef = theResDef;
myDef = null;
myParent = null;
}
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(StringBuilder thePathBuilder, boolean theStarPass) {
return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, myEncodeElementsAppliesToResourceTypes, myEncodeElements, true);
}
private boolean checkIfParentShouldNotBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, null, myDontEncodeElements, false);
}
private boolean checkIfPathMatchesForEncoding(StringBuilder thePathBuilder, boolean theStarPass, Set<String> theResourceTypes, Set<String> theElements, boolean theCheckingForWhitelist) {
if (myResDef != null) {
if (theResourceTypes != null) {
if (!theResourceTypes.contains(myResDef.getName())) {
return true;
}
}
if (theStarPass) {
thePathBuilder.append('*');
} else {
thePathBuilder.append(myResDef.getName());
}
if (theElements.contains(thePathBuilder.toString())) {
return true;
}
return false;
} else if (myParent != null) {
boolean parentCheck;
if (theCheckingForWhitelist) {
parentCheck = myParent.checkIfParentShouldBeEncodedAndBuildPath(thePathBuilder, theStarPass);
} else {
parentCheck = myParent.checkIfParentShouldNotBeEncodedAndBuildPath(thePathBuilder, theStarPass);
}
if (parentCheck) {
return true;
}
if (myDef != null) {
if (myDef.getMin() > 0) {
if (theElements.contains("*.(mandatory)")) {
return true;
}
}
thePathBuilder.append('.');
thePathBuilder.append(myDef.getElementName());
return theElements.contains(thePathBuilder.toString());
}
}
return true;
}
public BaseRuntimeChildDefinition getDef() {
return myDef;
}
public CompositeChildElement getParent() {
return myParent;
}
public RuntimeResourceDefinition getResDef() {
return myResDef;
}
public boolean shouldBeEncoded() {
boolean retVal = true;
if (myEncodeElements != null) {
retVal = checkIfParentShouldBeEncodedAndBuildPath(new StringBuilder(), false);
if (retVal == false && myEncodeElementsIncludesStars) {
retVal = checkIfParentShouldBeEncodedAndBuildPath(new StringBuilder(), true);
}
}
if (retVal && myDontEncodeElements != null) {
retVal = !checkIfParentShouldNotBeEncodedAndBuildPath(new StringBuilder(), false);
if (retVal && myDontEncodeElementsIncludesStars) {
retVal = !checkIfParentShouldNotBeEncodedAndBuildPath(new StringBuilder(), true);
}
}
// if (retVal == false && myEncodeElements.contains("*.(mandatory)")) {
// if (myDef.getMin() > 0) {
// retVal = true;
// }
// }
return retVal;
}
}
static class ContainedResources {
private long myNextContainedId = 1;
private List<IBaseResource> myResources = new ArrayList<IBaseResource>();
private IdentityHashMap<IBaseResource, IIdType> myResourceToId = new IdentityHashMap<IBaseResource, IIdType>();
public void addContained(IBaseResource theResource) {
if (myResourceToId.containsKey(theResource)) {
return;
}
IIdType newId;
if (theResource.getIdElement().isLocal()) {
newId = theResource.getIdElement();
} else {
// TODO: make this configurable between the two below (and something else?)
// newId = new IdDt(UUID.randomUUID().toString());
newId = new IdDt(myNextContainedId++);
}
myResourceToId.put(theResource, newId);
myResources.add(theResource);
}
public void addContained(IIdType theId, IBaseResource theResource) {
myResourceToId.put(theResource, theId);
myResources.add(theResource);
}
public List<IBaseResource> getContainedResources() {
return myResources;
}
public IIdType getResourceId(IBaseResource theNext) {
return myResourceToId.get(theNext);
}
public boolean isEmpty() {
return myResourceToId.isEmpty();
}
}
}