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Merge remote-tracking branch 'remotes/origin/master' into ks-subscription-delivery-queue-configurable-name

This commit is contained in:
Ken Stevens 2019-10-01 09:20:00 -04:00
parent 082dff71c2 48d191cbe5
commit ade9e0316e
21 changed files with 495 additions and 327 deletions
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10
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/BaseRuntimeChildDefinition.java
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@ -66,13 +66,17 @@ public abstract class BaseRuntimeChildDefinition {
} }
public interface IAccessor { public interface IAccessor {
List<IBase> getValues(Object theTarget); List<IBase> getValues(IBase theTarget);
default IBase getFirstValueOrNull(IBase theTarget) {
return getValues(theTarget).stream().findFirst().orElse(null);
}
} }
public interface IMutator { public interface IMutator {
void addValue(Object theTarget, IBase theValue); void addValue(IBase theTarget, IBase theValue);
void setValue(Object theTarget, IBase theValue); void setValue(IBase theTarget, IBase theValue);
} }
BaseRuntimeElementDefinition<?> findResourceReferenceDefinition(Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) { BaseRuntimeElementDefinition<?> findResourceReferenceDefinition(Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {

111
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/BaseRuntimeDeclaredChildDefinition.java
View File

@ -20,34 +20,33 @@ package ca.uhn.fhir.context;
* #L% * #L%
*/ */
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import java.lang.reflect.Field; import java.lang.reflect.Field;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.List; import java.util.List;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.util.ValidateUtil;
public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChildDefinition { public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChildDefinition {
private final IAccessor myAccessor; private final IAccessor myAccessor;
private String myBindingValueSet;
private final String myElementName; private final String myElementName;
private final Field myField; private final Field myField;
private final String myFormalDefinition; private final String myFormalDefinition;
private final int myMax; private final int myMax;
private final int myMin; private final int myMin;
private boolean myModifier;
private final IMutator myMutator; private final IMutator myMutator;
private final String myShortDefinition; private final String myShortDefinition;
private String myBindingValueSet;
private boolean myModifier;
private boolean mySummary; private boolean mySummary;
BaseRuntimeDeclaredChildDefinition(Field theField, Child theChildAnnotation, Description theDescriptionAnnotation, String theElementName) throws ConfigurationException { BaseRuntimeDeclaredChildDefinition(Field theField, Child theChildAnnotation, Description theDescriptionAnnotation, String theElementName) throws ConfigurationException {
super(); super();
Validate.notNull(theField, "No field speficied"); Validate.notNull(theField, "No field specified");
ValidateUtil.isGreaterThanOrEqualTo(theChildAnnotation.min(), 0, "Min must be >= 0"); ValidateUtil.isGreaterThanOrEqualTo(theChildAnnotation.min(), 0, "Min must be >= 0");
Validate.isTrue(theChildAnnotation.max() == -1 || theChildAnnotation.max() >= theChildAnnotation.min(), "Max must be >= Min (unless it is -1 / unlimited)"); Validate.isTrue(theChildAnnotation.max() == -1 || theChildAnnotation.max() >= theChildAnnotation.min(), "Max must be >= Min (unless it is -1 / unlimited)");
Validate.notBlank(theElementName, "Element name must not be blank"); Validate.notBlank(theElementName, "Element name must not be blank");
@ -87,6 +86,10 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
return myBindingValueSet; return myBindingValueSet;
} }
void setBindingValueSet(String theBindingValueSet) {
myBindingValueSet = theBindingValueSet;
}
@Override @Override
public String getElementName() { public String getElementName() {
return myElementName; return myElementName;
@ -119,107 +122,99 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
return myShortDefinition; return myShortDefinition;
} }
public BaseRuntimeElementDefinition<?> getSingleChildOrThrow() {
if (getValidChildNames().size() != 1) {
throw new IllegalStateException("This child has " + getValidChildNames().size() + " children, expected 1. This is a HAPI bug. Found: " + getValidChildNames());
}
return getChildByName(getValidChildNames().iterator().next());
}
public boolean isModifier() { public boolean isModifier() {
return myModifier; return myModifier;
} }
protected void setModifier(boolean theModifier) {
myModifier = theModifier;
}
@Override @Override
public boolean isSummary() { public boolean isSummary() {
return mySummary; return mySummary;
} }
void setBindingValueSet(String theBindingValueSet) {
myBindingValueSet = theBindingValueSet;
}
protected void setModifier(boolean theModifier) {
myModifier = theModifier;
}
private final class FieldListAccessor implements IAccessor { private final class FieldListAccessor implements IAccessor {
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
@Override @Override
public List<IBase> getValues(Object theTarget) { public List<IBase> getValues(IBase theTarget) {
List<IBase> retVal; List<IBase> retVal = (List<IBase>) getFieldValue(theTarget, myField);
try {
retVal = (List<IBase>) myField.get(theTarget);
} catch (Exception e) {
throw new ConfigurationException("Failed to get value", e);
}
if (retVal == null) { if (retVal == null) {
retVal = Collections.emptyList(); retVal = Collections.emptyList();
} }
return retVal; return retVal;
} }
} }
protected final class FieldListMutator implements IMutator { protected final class FieldListMutator implements IMutator {
@Override @Override
public void addValue(Object theTarget, IBase theValue) { public void addValue(IBase theTarget, IBase theValue) {
addValue(theTarget, theValue, false); addValue(theTarget, theValue, false);
} }
private void addValue(Object theTarget, IBase theValue, boolean theClear) { private void addValue(IBase theTarget, IBase theValue, boolean theClear) {
try {
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
List<IBase> existingList = (List<IBase>) myField.get(theTarget); List<IBase> existingList = (List<IBase>) getFieldValue(theTarget, myField);
if (existingList == null) { if (existingList == null) {
existingList = new ArrayList<IBase>(2); existingList = new ArrayList<>(2);
myField.set(theTarget, existingList); setFieldValue(theTarget, existingList, myField);
} }
if (theClear) { if (theClear) {
existingList.clear(); existingList.clear();
} }
existingList.add(theValue); existingList.add(theValue);
} catch (Exception e) {
throw new ConfigurationException("Failed to set value", e);
}
} }
@Override @Override
public void setValue(Object theTarget, IBase theValue) { public void setValue(IBase theTarget, IBase theValue) {
addValue(theTarget, theValue, true); addValue(theTarget, theValue, true);
} }
} }
private final class FieldPlainAccessor implements IAccessor { private final class FieldPlainAccessor implements IAccessor {
@Override @Override
public List<IBase> getValues(Object theTarget) { public List<IBase> getValues(IBase theTarget) {
try { Object values = getFieldValue(theTarget, myField);
Object values = myField.get(theTarget);
if (values == null) { if (values == null) {
return Collections.emptyList(); return Collections.emptyList();
} }
List<IBase> retVal = Collections.singletonList((IBase) values); return Collections.singletonList((IBase) values);
return retVal;
} catch (Exception e) {
throw new ConfigurationException("Failed to get value", e);
} }
@Override
public IBase getFirstValueOrNull(IBase theTarget) {
return (IBase) getFieldValue(theTarget, myField);
} }
} }
protected final class FieldPlainMutator implements IMutator { protected final class FieldPlainMutator implements IMutator {
@Override @Override
public void addValue(Object theTarget, IBase theValue) { public void addValue(IBase theTarget, IBase theValue) {
try { setFieldValue(theTarget, theValue, myField);
myField.set(theTarget, theValue);
} catch (Exception e) {
throw new ConfigurationException("Failed to set value", e);
}
} }
@Override @Override
public void setValue(Object theTarget, IBase theValue) { public void setValue(IBase theTarget, IBase theValue) {
addValue(theTarget, theValue); addValue(theTarget, theValue);
} }
} }
private static void setFieldValue(IBase theTarget, Object theValue, Field theField) {
try {
theField.set(theTarget, theValue);
} catch (IllegalAccessException e) {
throw new ConfigurationException("Failed to set value", e);
}
}
private static Object getFieldValue(IBase theTarget, Field theField) {
try {
return theField.get(theTarget);
} catch (IllegalAccessException e) {
throw new ConfigurationException("Failed to get value", e);
}
}
} }

7
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeChildUndeclaredExtensionDefinition.java
View File

@ -68,7 +68,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
public IAccessor getAccessor() { public IAccessor getAccessor() {
return new IAccessor() { return new IAccessor() {
@Override @Override
public List<IBase> getValues(Object theTarget) { public List<IBase> getValues(IBase theTarget) {
ExtensionDt target = (ExtensionDt) theTarget; ExtensionDt target = (ExtensionDt) theTarget;
if (target.getValue() != null) { if (target.getValue() != null) {
return Collections.singletonList((IBase) target.getValue()); return Collections.singletonList((IBase) target.getValue());
@ -76,6 +76,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
ArrayList<IBase> retVal = new ArrayList<IBase>(target.getUndeclaredExtensions()); ArrayList<IBase> retVal = new ArrayList<IBase>(target.getUndeclaredExtensions());
return retVal; return retVal;
} }
}; };
} }
@ -113,7 +114,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
public IMutator getMutator() { public IMutator getMutator() {
return new IMutator() { return new IMutator() {
@Override @Override
public void addValue(Object theTarget, IBase theValue) { public void addValue(IBase theTarget, IBase theValue) {
ExtensionDt target = (ExtensionDt) theTarget; ExtensionDt target = (ExtensionDt) theTarget;
if (theValue instanceof IDatatype) { if (theValue instanceof IDatatype) {
target.setValue((IDatatype) theTarget); target.setValue((IDatatype) theTarget);
@ -123,7 +124,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
} }
@Override @Override
public void setValue(Object theTarget, IBase theValue) { public void setValue(IBase theTarget, IBase theValue) {
ExtensionDt target = (ExtensionDt) theTarget; ExtensionDt target = (ExtensionDt) theTarget;
if (theValue instanceof IDatatype) { if (theValue instanceof IDatatype) {
target.setValue((IDatatype) theTarget); target.setValue((IDatatype) theTarget);

111
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
View File

@ -19,17 +19,6 @@ package ca.uhn.fhir.parser;
* limitations under the License. * limitations under the License.
* #L% * #L%
*/ */
import static org.apache.commons.lang3.StringUtils.*;
import java.util.*;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;
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.*;
import ca.uhn.fhir.context.*; import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition.IMutator; import ca.uhn.fhir.context.BaseRuntimeChildDefinition.IMutator;
@ -37,21 +26,32 @@ import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.api.annotation.Child; import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt; import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.base.resource.ResourceMetadataMap; import ca.uhn.fhir.model.base.resource.ResourceMetadataMap;
import ca.uhn.fhir.model.primitive.*; import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.XhtmlDt;
import ca.uhn.fhir.parser.json.JsonLikeValue.ScalarType; import ca.uhn.fhir.parser.json.JsonLikeValue.ScalarType;
import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType; import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
import ca.uhn.fhir.util.*; import ca.uhn.fhir.util.*;
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.*;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.*;
class ParserState<T> { class ParserState<T> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ParserState.class); private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ParserState.class);
private List<String> myComments = new ArrayList<String>(2);
private final FhirContext myContext; private final FhirContext myContext;
private final IParserErrorHandler myErrorHandler; private final IParserErrorHandler myErrorHandler;
private final boolean myJsonMode; private final boolean myJsonMode;
private T myObject;
private final IParser myParser; private final IParser myParser;
private List<String> myComments = new ArrayList<String>(2);
private T myObject;
private IBase myPreviousElement; private IBase myPreviousElement;
private BaseState myState; private BaseState myState;
@ -152,38 +152,6 @@ class ParserState<T> {
} }
} }
/**
* @param theResourceType
* May be null
*/
static <T extends IBaseResource> ParserState<T> getPreResourceInstance(IParser theParser, Class<T> theResourceType, FhirContext theContext, boolean theJsonMode, IParserErrorHandler theErrorHandler)
throws DataFormatException {
ParserState<T> retVal = new ParserState<T>(theParser, theContext, theJsonMode, theErrorHandler);
if (theResourceType == null) {
if (theContext.getVersion().getVersion().isRi()) {
retVal.push(retVal.new PreResourceStateHl7Org(theResourceType));
} else {
retVal.push(retVal.new PreResourceStateHapi(theResourceType));
}
} else {
if (IResource.class.isAssignableFrom(theResourceType)) {
retVal.push(retVal.new PreResourceStateHapi(theResourceType));
} else {
retVal.push(retVal.new PreResourceStateHl7Org(theResourceType));
}
}
return retVal;
}
static ParserState<TagList> getPreTagListInstance(IParser theParser, FhirContext theContext, boolean theJsonMode, IParserErrorHandler theErrorHandler) {
ParserState<TagList> retVal = new ParserState<TagList>(theParser, theContext, theJsonMode, theErrorHandler);
retVal.push(retVal.new PreTagListState());
return retVal;
}
private abstract class BaseState { private abstract class BaseState {
private PreResourceState myPreResourceState; private PreResourceState myPreResourceState;
@ -195,8 +163,7 @@ class ParserState<T> {
} }
/** /**
* @param theValue * @param theValue The attribute value
* The attribute value
*/ */
public void attributeValue(String theName, String theValue) throws DataFormatException { public void attributeValue(String theName, String theValue) throws DataFormatException {
myErrorHandler.unknownAttribute(null, theName); myErrorHandler.unknownAttribute(null, theName);
@ -211,8 +178,7 @@ class ParserState<T> {
} }
/** /**
* @param theNamespaceUri * @param theNamespaceUri The XML namespace (if XML) or null
* The XML namespace (if XML) or null
*/ */
public void enteringNewElement(String theNamespaceUri, String theLocalPart) throws DataFormatException { public void enteringNewElement(String theNamespaceUri, String theLocalPart) throws DataFormatException {
myErrorHandler.unknownElement(null, theLocalPart); myErrorHandler.unknownElement(null, theLocalPart);
@ -275,8 +241,7 @@ class ParserState<T> {
} }
/** /**
* @param theData * @param theData The string value
* The string value
*/ */
public void string(String theData) { public void string(String theData) {
// ignore by default // ignore by default
@ -287,8 +252,7 @@ class ParserState<T> {
} }
/** /**
* @param theNextEvent * @param theNextEvent The XML event
* The XML event
*/ */
public void xmlEvent(XMLEvent theNextEvent) { public void xmlEvent(XMLEvent theNextEvent) {
// ignore // ignore
@ -890,7 +854,6 @@ class ParserState<T> {
} }
private abstract class PreResourceState extends BaseState { private abstract class PreResourceState extends BaseState {
private Map<String, IBaseResource> myContainedResources; private Map<String, IBaseResource> myContainedResources;
@ -1137,7 +1100,7 @@ class ParserState<T> {
private class PreResourceStateHapi extends PreResourceState { private class PreResourceStateHapi extends PreResourceState {
private IMutator myMutator; private IMutator myMutator;
private Object myTarget; private IBase myTarget;
public PreResourceStateHapi(Class<? extends IBaseResource> theResourceType) { public PreResourceStateHapi(Class<? extends IBaseResource> theResourceType) {
@ -1145,7 +1108,7 @@ class ParserState<T> {
assert theResourceType == null || IResource.class.isAssignableFrom(theResourceType); assert theResourceType == null || IResource.class.isAssignableFrom(theResourceType);
} }
public PreResourceStateHapi(Object theTarget, IMutator theMutator, Class<? extends IBaseResource> theResourceType) { public PreResourceStateHapi(IBase theTarget, IMutator theMutator, Class<? extends IBaseResource> theResourceType) {
super(theResourceType); super(theResourceType);
myTarget = theTarget; myTarget = theTarget;
myMutator = theMutator; myMutator = theMutator;
@ -1195,13 +1158,13 @@ class ParserState<T> {
private class PreResourceStateHl7Org extends PreResourceState { private class PreResourceStateHl7Org extends PreResourceState {
private IMutator myMutator; private IMutator myMutator;
private Object myTarget; private IBase myTarget;
public PreResourceStateHl7Org(Class<? extends IBaseResource> theResourceType) { public PreResourceStateHl7Org(Class<? extends IBaseResource> theResourceType) {
super(theResourceType); super(theResourceType);
} }
public PreResourceStateHl7Org(Object theTarget, IMutator theMutator, Class<? extends IBaseResource> theResourceType) { public PreResourceStateHl7Org(IBase theTarget, IMutator theMutator, Class<? extends IBaseResource> theResourceType) {
super(theResourceType); super(theResourceType);
myMutator = theMutator; myMutator = theMutator;
myTarget = theTarget; myTarget = theTarget;
@ -1604,4 +1567,32 @@ class ParserState<T> {
} }
/**
* @param theResourceType May be null
*/
static <T extends IBaseResource> ParserState<T> getPreResourceInstance(IParser theParser, Class<T> theResourceType, FhirContext theContext, boolean theJsonMode, IParserErrorHandler theErrorHandler)
throws DataFormatException {
ParserState<T> retVal = new ParserState<T>(theParser, theContext, theJsonMode, theErrorHandler);
if (theResourceType == null) {
if (theContext.getVersion().getVersion().isRi()) {
retVal.push(retVal.new PreResourceStateHl7Org(theResourceType));
} else {
retVal.push(retVal.new PreResourceStateHapi(theResourceType));
}
} else {
if (IResource.class.isAssignableFrom(theResourceType)) {
retVal.push(retVal.new PreResourceStateHapi(theResourceType));
} else {
retVal.push(retVal.new PreResourceStateHl7Org(theResourceType));
}
}
return retVal;
}
static ParserState<TagList> getPreTagListInstance(IParser theParser, FhirContext theContext, boolean theJsonMode, IParserErrorHandler theErrorHandler) {
ParserState<TagList> retVal = new ParserState<TagList>(theParser, theContext, theJsonMode, theErrorHandler);
retVal.push(retVal.new PreTagListState());
return retVal;
}
} }

13
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
View File

@ -354,17 +354,10 @@ public class XmlParser extends BaseParser {
} }
if (nextChild instanceof RuntimeChildNarrativeDefinition) { if (nextChild instanceof RuntimeChildNarrativeDefinition) {
INarrative narr = (INarrative) nextChild.getAccessor().getFirstValueOrNull(theElement);
INarrativeGenerator gen = myContext.getNarrativeGenerator(); INarrativeGenerator gen = myContext.getNarrativeGenerator();
INarrative narr; if (gen != null && (narr == null || narr.isEmpty())) {
if (theResource instanceof IResource) {
narr = ((IResource) theResource).getText();
} else if (theResource instanceof IDomainResource) {
narr = ((IDomainResource) theResource).getText();
} else {
narr = null;
}
// FIXME potential null access on narr see line 623
if (gen != null && narr.isEmpty()) {
gen.populateResourceNarrative(myContext, theResource); gen.populateResourceNarrative(myContext, theResource);
} }
if (narr != null && narr.isEmpty() == false) { if (narr != null && narr.isEmpty() == false) {

33
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -216,12 +216,12 @@ public class FhirTerser {
} }
public Object getSingleValueOrNull(IBase theTarget, String thePath) { public Object getSingleValueOrNull(IBase theTarget, String thePath) {
Class<Object> wantedType = Object.class; Class<IBase> wantedType = IBase.class;
return getSingleValueOrNull(theTarget, thePath, wantedType); return getSingleValueOrNull(theTarget, thePath, wantedType);
} }
public <T> T getSingleValueOrNull(IBase theTarget, String thePath, Class<T> theWantedType) { public <T extends IBase> T getSingleValueOrNull(IBase theTarget, String thePath, Class<T> theWantedType) {
Validate.notNull(theTarget, "theTarget must not be null"); Validate.notNull(theTarget, "theTarget must not be null");
Validate.notBlank(thePath, "thePath must not be empty"); Validate.notBlank(thePath, "thePath must not be empty");
@ -241,12 +241,12 @@ public class FhirTerser {
return retVal.get(0); return retVal.get(0);
} }
private <T> List<T> getValues(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, Object theCurrentObj, List<String> theSubList, Class<T> theWantedClass) { private <T extends IBase> List<T> getValues(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, IBase theCurrentObj, List<String> theSubList, Class<T> theWantedClass) {
return getValues(theCurrentDef, theCurrentObj, theSubList, theWantedClass, false, false); return getValues(theCurrentDef, theCurrentObj, theSubList, theWantedClass, false, false);
} }
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
private <T> List<T> getValues(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, Object theCurrentObj, List<String> theSubList, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) { private <T extends IBase> List<T> getValues(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, IBase theCurrentObj, List<String> theSubList, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) {
String name = theSubList.get(0); String name = theSubList.get(0);
List<T> retVal = new ArrayList<>(); List<T> retVal = new ArrayList<>();
@ -325,7 +325,7 @@ public class FhirTerser {
List<T> values = retVal; List<T> values = retVal;
retVal = new ArrayList<>(); retVal = new ArrayList<>();
for (T nextElement : values) { for (T nextElement : values) {
BaseRuntimeElementCompositeDefinition<?> nextChildDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition((Class<? extends IBase>) nextElement.getClass()); BaseRuntimeElementCompositeDefinition<?> nextChildDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(nextElement.getClass());
List<T> foundValues = getValues(nextChildDef, nextElement, theSubList.subList(1, theSubList.size()), theWantedClass, theCreate, theAddExtension); List<T> foundValues = getValues(nextChildDef, nextElement, theSubList.subList(1, theSubList.size()), theWantedClass, theCreate, theAddExtension);
retVal.addAll(foundValues); retVal.addAll(foundValues);
} }
@ -410,7 +410,7 @@ public class FhirTerser {
List<T> values = retVal; List<T> values = retVal;
retVal = new ArrayList<>(); retVal = new ArrayList<>();
for (T nextElement : values) { for (T nextElement : values) {
BaseRuntimeElementCompositeDefinition<?> nextChildDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition((Class<? extends IBase>) nextElement.getClass()); BaseRuntimeElementCompositeDefinition<?> nextChildDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(nextElement.getClass());
List<T> foundValues = getValues(nextChildDef, nextElement, theSubList.subList(1, theSubList.size()), theWantedClass, theCreate, theAddExtension); List<T> foundValues = getValues(nextChildDef, nextElement, theSubList.subList(1, theSubList.size()), theWantedClass, theCreate, theAddExtension);
retVal.addAll(foundValues); retVal.addAll(foundValues);
} }
@ -476,9 +476,10 @@ public class FhirTerser {
* @return A list of values of type {@link Object}. * @return A list of values of type {@link Object}.
*/ */
public List<Object> getValues(IBaseResource theResource, String thePath) { public List<Object> getValues(IBaseResource theResource, String thePath) {
Class<Object> wantedClass = Object.class; Class<IBase> wantedClass = IBase.class;
return getValues(theResource, thePath, wantedClass); List values = getValues(theResource, thePath, wantedClass);
return values;
} }
/** /**
@ -491,9 +492,10 @@ public class FhirTerser {
* @return A list of values of type {@link Object}. * @return A list of values of type {@link Object}.
*/ */
public List<Object> getValues(IBaseResource theResource, String thePath, boolean theCreate) { public List<Object> getValues(IBaseResource theResource, String thePath, boolean theCreate) {
Class<Object> wantedClass = Object.class; Class<IBase> wantedClass = IBase.class;
return getValues(theResource, thePath, wantedClass, theCreate); List retVal = getValues(theResource, thePath, wantedClass, theCreate);
return retVal;
} }
/** /**
@ -507,9 +509,10 @@ public class FhirTerser {
* @return A list of values of type {@link Object}. * @return A list of values of type {@link Object}.
*/ */
public List<Object> getValues(IBaseResource theResource, String thePath, boolean theCreate, boolean theAddExtension) { public List<Object> getValues(IBaseResource theResource, String thePath, boolean theCreate, boolean theAddExtension) {
Class<Object> wantedClass = Object.class; Class<IBase> wantedClass = IBase.class;
return getValues(theResource, thePath, wantedClass, theCreate, theAddExtension); List retVal = getValues(theResource, thePath, wantedClass, theCreate, theAddExtension);
return retVal;
} }
/** /**
@ -522,7 +525,7 @@ public class FhirTerser {
* @param <T> Type declared by <code>theWantedClass</code> * @param <T> Type declared by <code>theWantedClass</code>
* @return A list of values of type <code>theWantedClass</code>. * @return A list of values of type <code>theWantedClass</code>.
*/ */
public <T> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass) { public <T extends IBase> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass) {
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource); RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
List<String> parts = parsePath(def, thePath); List<String> parts = parsePath(def, thePath);
return getValues(def, theResource, parts, theWantedClass); return getValues(def, theResource, parts, theWantedClass);
@ -539,7 +542,7 @@ public class FhirTerser {
* @param <T> Type declared by <code>theWantedClass</code> * @param <T> Type declared by <code>theWantedClass</code>
* @return A list of values of type <code>theWantedClass</code>. * @return A list of values of type <code>theWantedClass</code>.
*/ */
public <T> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate) { public <T extends IBase> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate) {
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource); RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
List<String> parts = parsePath(def, thePath); List<String> parts = parsePath(def, thePath);
return getValues(def, theResource, parts, theWantedClass, theCreate, false); return getValues(def, theResource, parts, theWantedClass, theCreate, false);
@ -557,7 +560,7 @@ public class FhirTerser {
* @param <T> Type declared by <code>theWantedClass</code> * @param <T> Type declared by <code>theWantedClass</code>
* @return A list of values of type <code>theWantedClass</code>. * @return A list of values of type <code>theWantedClass</code>.
*/ */
public <T> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) { public <T extends IBase> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) {
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource); RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
List<String> parts = parsePath(def, thePath); List<String> parts = parsePath(def, thePath);
return getValues(def, theResource, parts, theWantedClass, theCreate, theAddExtension); return getValues(def, theResource, parts, theWantedClass, theCreate, theAddExtension);

12
hapi-fhir-jpaserver-base/pom.xml
View File

@ -276,6 +276,12 @@
<groupId>org.apache.commons</groupId> <groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId> <artifactId>commons-dbcp2</artifactId>
<scope>test</scope> <scope>test</scope>
<exclusions>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
</dependency> </dependency>
<dependency> <dependency>
<groupId>junit</groupId> <groupId>junit</groupId>
@ -500,6 +506,12 @@
<dependency> <dependency>
<groupId>org.hibernate</groupId> <groupId>org.hibernate</groupId>
<artifactId>hibernate-search-elasticsearch</artifactId> <artifactId>hibernate-search-elasticsearch</artifactId>
<exclusions>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
</dependency> </dependency>
<!-- Misc --> <!-- Misc -->

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IJpaDao.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.dao; package ca.uhn.fhir.jpa.dao;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 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 ca.uhn.fhir.jpa.model.entity.ResourceTable; import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/ElasticsearchHibernatePropertiesBuilder.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.search.elastic; package ca.uhn.fhir.jpa.search.elastic;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 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 org.hibernate.search.cfg.Environment; import org.hibernate.search.cfg.Environment;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchEnvironment; import org.hibernate.search.elasticsearch.cfg.ElasticsearchEnvironment;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus; import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/ElasticsearchMappingProvider.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.search.elastic;
/*- /*-
* #%L * #%L
* HAPI FHIR JPA Server - ElasticSearch Integration * HAPI FHIR JPA Server
* %% * %%
* Copyright (C) 2014 - 2019 University Health Network * Copyright (C) 2014 - 2019 University Health Network
* %% * %%

7
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -80,7 +80,6 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
bulkExportJob.addIndex("IDX_BLKEX_EXPTIME").unique(false).withColumns("EXP_TIME"); bulkExportJob.addIndex("IDX_BLKEX_EXPTIME").unique(false).withColumns("EXP_TIME");
bulkExportJob.addIndex("IDX_BLKEX_JOB_ID").unique(true).withColumns("JOB_ID"); bulkExportJob.addIndex("IDX_BLKEX_JOB_ID").unique(true).withColumns("JOB_ID");
// HFJ_BLK_EXPORT_COLLECTION // HFJ_BLK_EXPORT_COLLECTION
version.addIdGenerator("SEQ_BLKEXCOL_PID"); version.addIdGenerator("SEQ_BLKEXCOL_PID");
Builder.BuilderAddTableByColumns bulkExportCollection = version.addTableByColumns("HFJ_BLK_EXPORT_COLLECTION", "PID"); Builder.BuilderAddTableByColumns bulkExportCollection = version.addTableByColumns("HFJ_BLK_EXPORT_COLLECTION", "PID");
@ -99,7 +98,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
bulkExportCollectionFile.addColumn("RES_ID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100); bulkExportCollectionFile.addColumn("RES_ID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
bulkExportCollectionFile.addForeignKey("FK_BLKEXCOLFILE_COLLECT").toColumn("COLLECTION_PID").references("HFJ_BLK_EXPORT_COLLECTION", "PID"); bulkExportCollectionFile.addForeignKey("FK_BLKEXCOLFILE_COLLECT").toColumn("COLLECTION_PID").references("HFJ_BLK_EXPORT_COLLECTION", "PID");
// HFJ_RES_VER_PROV
version.startSectionWithMessage("Processing bulkExportCollectionFile: HFJ_RES_VER_PROV"); version.startSectionWithMessage("Processing bulkExportCollectionFile: HFJ_RES_VER_PROV");
Builder.BuilderAddTableByColumns resVerProv = version.addTableByColumns("HFJ_RES_VER_PROV", "RES_VER_PID"); Builder.BuilderAddTableByColumns resVerProv = version.addTableByColumns("HFJ_RES_VER_PROV", "RES_VER_PID");
resVerProv.addColumn("RES_VER_PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG); resVerProv.addColumn("RES_VER_PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
@ -149,7 +148,6 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.unique(true) .unique(true)
.withColumns("VALUESET_PID", "VALUESET_ORDER"); .withColumns("VALUESET_PID", "VALUESET_ORDER");
// Account for RESTYPE_LEN column increasing from 30 to 35 // Account for RESTYPE_LEN column increasing from 30 to 35
version.onTable("HFJ_RESOURCE").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 35); version.onTable("HFJ_RESOURCE").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 35);
version.onTable("HFJ_HISTORY_TAG").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 35); version.onTable("HFJ_HISTORY_TAG").modifyColumn("RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 35);
@ -165,8 +163,9 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
version.startSectionWithMessage("Processing table: TRM_VALUESET_C_DESIGNATION"); version.startSectionWithMessage("Processing table: TRM_VALUESET_C_DESIGNATION");
version.onTable("TRM_VALUESET_C_DESIGNATION").modifyColumn("VAL").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 2000); version.onTable("TRM_VALUESET_C_DESIGNATION").modifyColumn("VAL").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 2000);
// TermConceptProperty
version.startSectionWithMessage("Processing table: TRM_CONCEPT_PROPERTY"); version.startSectionWithMessage("Processing table: TRM_CONCEPT_PROPERTY");
version.onTable("TRM_CONCEPT_PROPERTY").addColumn("PROP_VAL_LOB").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.CLOB); version.onTable("TRM_CONCEPT_PROPERTY").addColumn("PROP_VAL_LOB").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.BLOB);
} }
protected void init400() { protected void init400() {

23
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -319,6 +319,29 @@ public class JsonParserDstu3Test {
} }
/**
* See #402
*/
@Test
public void testEncodeCompositionDoesntOverwriteNarrative() {
FhirContext ctx = FhirContext.forDstu3();
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
Composition composition = new Composition();
composition.getText().setDivAsString("<div>root</div>");
composition.addSection().getText().setDivAsString("<div>section0</div>");
composition.addSection().getText().setDivAsString("<div>section1</div>");
String output = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(composition);
ourLog.info(output);
assertThat(output, containsString("<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">root</div>"));
assertThat(output, containsString("<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">section0</div>"));
assertThat(output, containsString("<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">section1</div>"));
}
@Test @Test
public void testEncodeAndParseMetaProfileAndTags() { public void testEncodeAndParseMetaProfileAndTags() {
Patient p = new Patient(); Patient p = new Patient();

22
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
View File

@ -1070,6 +1070,28 @@ public class XmlParserDstu3Test {
assertEquals("grandparent", gp.getName()); assertEquals("grandparent", gp.getName());
} }
/**
* See #402
*/
@Test
public void testEncodeCompositionDoesntOverwriteNarrative() {
FhirContext ctx = FhirContext.forDstu3();
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
Composition composition = new Composition();
composition.getText().setDivAsString("<div>root</div>");
composition.addSection().getText().setDivAsString("<div>section0</div>");
composition.addSection().getText().setDivAsString("<div>section1</div>");
String output = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(composition);
ourLog.info(output);
assertThat(output, containsString("<div xmlns=\"http://www.w3.org/1999/xhtml\">root</div>"));
assertThat(output, containsString("<div xmlns=\"http://www.w3.org/1999/xhtml\">section0</div>"));
assertThat(output, containsString("<div xmlns=\"http://www.w3.org/1999/xhtml\">section1</div>"));
}
/** /**
* See #326 * See #326
*/ */

28
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
View File

@ -448,6 +448,34 @@ public class JsonParserR4Test {
} }
private Composition createComposition(String sectionText) {
Composition c = new Composition();
Narrative compositionText = new Narrative().setStatus(Narrative.NarrativeStatus.GENERATED);
compositionText.setDivAsString("Composition");
Narrative compositionSectionText = new Narrative().setStatus(Narrative.NarrativeStatus.GENERATED);
compositionSectionText.setDivAsString(sectionText);
c.setText(compositionText);
c.addSection().setText(compositionSectionText);
return c;
}
/**
* See #402 (however JSON is fine)
*/
@Test
public void testEncodingTextSection() {
String sectionText = "sectionText";
Composition composition = createComposition(sectionText);
String encoded = ourCtx.newJsonParser().encodeResourceToString(composition);
ourLog.info(encoded);
int idx = encoded.indexOf(sectionText);
assertNotEquals(-1, idx);
}
/** /**
* 2019-09-19 - Pre #1489 * 2019-09-19 - Pre #1489
* 18:24:48.548 [main] INFO ca.uhn.fhir.parser.JsonParserR4Test [JsonParserR4Test.java:483] - Encoded 200 passes - 50ms / pass - 19.7 / second * 18:24:48.548 [main] INFO ca.uhn.fhir.parser.JsonParserR4Test [JsonParserR4Test.java:483] - Encoded 200 passes - 50ms / pass - 19.7 / second

45
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/XmlParserR4Test.java Normal file
View File

@ -0,0 +1,45 @@
package ca.uhn.fhir.parser;
import static org.junit.Assert.assertNotEquals;
import org.hl7.fhir.r4.model.Composition;
import org.hl7.fhir.r4.model.Narrative;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import ca.uhn.fhir.context.FhirContext;
public class XmlParserR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(XmlParserR4Test.class);
private static FhirContext ourCtx = FhirContext.forR4();
private Composition createComposition(String sectionText) {
Composition c = new Composition();
Narrative compositionText = new Narrative().setStatus(Narrative.NarrativeStatus.GENERATED);
compositionText.setDivAsString("Composition");
Narrative compositionSectionText = new Narrative().setStatus(Narrative.NarrativeStatus.GENERATED);
compositionSectionText.setDivAsString(sectionText);
c.setText(compositionText);
c.addSection().setText(compositionSectionText);
return c;
}
/**
* See #402 section.text is overwritten by composition.text
*/
@Test
public void testEncodingTextSection() {
String sectionText = "sectionText";
Composition composition = createComposition(sectionText);
String encoded = ourCtx.newXmlParser().encodeResourceToString(composition);
ourLog.info(encoded);
int idx = encoded.indexOf(sectionText);
assertNotEquals(-1, idx);
}
}

2
hapi-fhir-testpage-overlay/src/main/webapp/WEB-INF/templates/tmpl-head.html
View File

@ -20,7 +20,7 @@
<script th:src="@{/fa/js/all.min.js}" data-auto-replace-svg="nest"></script> <script th:src="@{/fa/js/all.min.js}" data-auto-replace-svg="nest"></script>
<link href="css/hapi-narrative.css" rel="stylesheet"/> <link href="css/hapi-narrative.css" rel="stylesheet"/>
<script type="text/javascript" src="js/moment.min.js"></script> <script type="text/javascript" src="js/moment-with-locales.min.js"></script>
<link href="css/bootstrap-datetimepicker.min.css" rel="stylesheet"/> <link href="css/bootstrap-datetimepicker.min.css" rel="stylesheet"/>
<script src="js/bootstrap-datetimepicker.min.js"></script> <script src="js/bootstrap-datetimepicker.min.js"></script>
<link href="css/select2.css" rel="stylesheet"/> <link href="css/select2.css" rel="stylesheet"/>

4
hapi-fhir-testpage-overlay/src/main/webapp/js/RestfulTester.js
View File

@ -331,8 +331,8 @@ function addSearchControlDate(theSearchParamName, theContainerRowNum, theRowNum,
) )
); );
input.datetimepicker({ input.datetimepicker({
pickTime: false, format: "YYYY-MM-DD",
showToday: true showTodayButton: true
}); });
// Set up the qualifier dropdown after we've initialized the datepicker, since it // Set up the qualifier dropdown after we've initialized the datepicker, since it
// overrides all addon buttons while it inits.. // overrides all addon buttons while it inits..

6
hapi-fhir-testpage-overlay/src/main/webapp/js/moment-with-locales.min.js vendored Normal file
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File diff suppressed because one or more lines are too long

6
hapi-fhir-testpage-overlay/src/main/webapp/js/moment.min.js vendored
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File diff suppressed because one or more lines are too long

3
pom.xml
View File

@ -552,6 +552,9 @@
<id>dmap</id> <id>dmap</id>
<name>David Maplesden</name> <name>David Maplesden</name>
</developer> </developer>
<developer>
<id>jaferkhan</id>
</developer>
</developers> </developers>
<licenses> <licenses>

9
src/changes/changes.xml
View File

@ -287,6 +287,15 @@
conditional creates can now be authorized even if they are happening inside a FHIR conditional creates can now be authorized even if they are happening inside a FHIR
transaction. transaction.
</action> </action>
<action type="fix" issue="402">
When encoding a Composition resource in XML, the section narrative blocks were incorrectly
replaced by the main resource narrative. Thanks to Mirjam Baltus for reporting!
</action>
<action type="fix" issue="1473">
AN issue with date pickers not working in the hapi-fhir-testpage-overlay
project has been fixed. Thanks to GitHub user @jaferkhan for the pull
request!
</action>
</release> </release>
<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)"> <release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
<action type="fix"> <action type="fix">