Improve parallel model scanning (#3046)
* Improve parallel model scanning * Add changelog * Resolve fixme * Test fix
This commit is contained in:
James Agnew
GitHub
parent
53a2d3c1ac
commit
95e853bdf7
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@ -1,57 +1,5 @@
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package ca.uhn.fhir.context;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import java.lang.reflect.Field;
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import java.lang.reflect.Modifier;
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/*
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* #%L
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* HAPI FHIR - Core Library
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* %%
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* Copyright (C) 2014 - 2021 Smile CDR, Inc.
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.LinkedList;
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import java.util.List;
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import java.util.ListIterator;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.TreeMap;
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import java.util.TreeSet;
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import org.apache.commons.lang3.builder.ToStringBuilder;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
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import org.hl7.fhir.instance.model.api.IBaseDatatype;
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import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
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import org.hl7.fhir.instance.model.api.IBaseEnumeration;
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import org.hl7.fhir.instance.model.api.IBaseExtension;
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import org.hl7.fhir.instance.model.api.IBaseReference;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.ICompositeType;
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import org.hl7.fhir.instance.model.api.INarrative;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import ca.uhn.fhir.model.api.IBoundCodeableConcept;
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import ca.uhn.fhir.model.api.IDatatype;
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import ca.uhn.fhir.model.api.IElement;
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@ -69,18 +17,47 @@ import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
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import ca.uhn.fhir.model.primitive.BoundCodeDt;
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import ca.uhn.fhir.parser.DataFormatException;
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import ca.uhn.fhir.util.ReflectionUtil;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
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import org.hl7.fhir.instance.model.api.IBaseDatatype;
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import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
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import org.hl7.fhir.instance.model.api.IBaseEnumeration;
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import org.hl7.fhir.instance.model.api.IBaseExtension;
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import org.hl7.fhir.instance.model.api.IBaseReference;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.ICompositeType;
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import org.hl7.fhir.instance.model.api.INarrative;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import java.lang.reflect.Field;
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import java.lang.reflect.Modifier;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.LinkedList;
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import java.util.List;
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import java.util.ListIterator;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.TreeMap;
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import java.util.TreeSet;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> extends BaseRuntimeElementDefinition<T> {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseRuntimeElementCompositeDefinition.class);
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private final FhirContext myContext;
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private Map<String, Integer> forcedOrder = null;
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private List<BaseRuntimeChildDefinition> myChildren = new ArrayList<>();
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private List<BaseRuntimeChildDefinition> myChildrenAndExtensions;
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private Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinitions;
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private final FhirContext myContext;
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private Map<String, BaseRuntimeChildDefinition> myNameToChild = new HashMap<>();
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private List<ScannedField> myScannedFields = new ArrayList<>();
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private volatile boolean mySealed;
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private volatile SealingStateEnum mySealed = SealingStateEnum.NOT_SEALED;
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@SuppressWarnings("unchecked")
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public BaseRuntimeElementCompositeDefinition(String theName, Class<? extends T> theImplementingClass, boolean theStandardType, FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
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@ -174,7 +151,7 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
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* Has this class been sealed
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*/
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public boolean isSealed() {
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return mySealed;
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return mySealed == SealingStateEnum.SEALED;
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}
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@SuppressWarnings("unchecked")
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@ -459,12 +436,18 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
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elementNames.add(elementName);
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}
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}
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@Override
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void sealAndInitialize(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
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if (mySealed) {
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if (mySealed == SealingStateEnum.SEALED) {
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return;
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}
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mySealed = true;
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synchronized (myContext) {
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if (mySealed == SealingStateEnum.SEALED || mySealed == SealingStateEnum.SEALING) {
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return;
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}
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mySealed = SealingStateEnum.SEALING;
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scanCompositeElementForChildren();
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@ -531,29 +514,26 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
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}
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myChildrenAndExtensions = Collections.unmodifiableList(children);
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mySealed = SealingStateEnum.SEALED;
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}
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}
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@Override
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protected void validateSealed() {
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if (!mySealed) {
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if (mySealed != SealingStateEnum.SEALED) {
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synchronized (myContext) {
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if(!mySealed) {
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if (mySealed == SealingStateEnum.NOT_SEALED) {
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sealAndInitialize(myContext, myClassToElementDefinitions);
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}
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}
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}
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}
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private static int findIndex(List<BaseRuntimeChildDefinition> theChildren, String theName, boolean theDefaultAtEnd) {
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int index = theDefaultAtEnd ? theChildren.size() : -1;
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for (ListIterator<BaseRuntimeChildDefinition> iter = theChildren.listIterator(); iter.hasNext(); ) {
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if (iter.next().getElementName().equals(theName)) {
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index = iter.previousIndex();
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break;
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}
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}
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return index;
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private enum SealingStateEnum {
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NOT_SEALED,
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SEALING,
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SEALED
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}
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private static class ScannedField {
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@ -563,6 +543,7 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
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private Class<?> myElementType;
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private Field myField;
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private boolean myFirstFieldInNewClass;
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ScannedField(Field theField, Class<?> theClass, boolean theFirstFieldInNewClass) {
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myField = theField;
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myFirstFieldInNewClass = theFirstFieldInNewClass;
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@ -609,4 +590,15 @@ public abstract class BaseRuntimeElementCompositeDefinition<T extends IBase> ext
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}
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}
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private static int findIndex(List<BaseRuntimeChildDefinition> theChildren, String theName, boolean theDefaultAtEnd) {
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int index = theDefaultAtEnd ? theChildren.size() : -1;
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for (ListIterator<BaseRuntimeChildDefinition> iter = theChildren.listIterator(); iter.hasNext(); ) {
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if (iter.next().getElementName().equals(theName)) {
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index = iter.previousIndex();
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break;
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}
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}
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return index;
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}
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}
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@ -224,9 +224,8 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
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/*
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* this does nothing, but BaseRuntimeElementCompositeDefinition
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* overrides this method to provide functionality because that class
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* defers the dealing process
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* defers the sealing process
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*/
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}
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public BaseRuntimeChildDefinition getChildByName(String theChildName) {
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@ -988,7 +988,8 @@ public class FhirTerser {
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case RESOURCE_BLOCK:
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case COMPOSITE_DATATYPE: {
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BaseRuntimeElementCompositeDefinition<?> childDef = (BaseRuntimeElementCompositeDefinition<?>) def;
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for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {
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List<BaseRuntimeChildDefinition> childrenAndExtensionDefs = childDef.getChildrenAndExtension();
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for (BaseRuntimeChildDefinition nextChild : childrenAndExtensionDefs) {
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List<?> values = nextChild.getAccessor().getValues(theElement);
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@ -0,0 +1,4 @@
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---
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type: fix
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issue: 3046
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title: When using deferred model scanning in highly parallelized environments, a crash could sometimes occur during parse/serialize operations.
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@ -58,6 +58,8 @@ import java.util.concurrent.TimeUnit;
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import java.util.concurrent.atomic.AtomicReference;
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import static org.hamcrest.CoreMatchers.containsString;
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import static org.hamcrest.CoreMatchers.either;
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import static org.hamcrest.CoreMatchers.equalTo;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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@ -228,7 +230,7 @@ public class InterceptorDstu3Test {
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httpPost.setEntity(new StringEntity(input, ContentType.create(Constants.CT_FHIR_JSON, "UTF-8")));
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HttpResponse status = ourClient.execute(httpPost);
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try {
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assertEquals(201, status.getStatusLine().getStatusCode());
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assertThat(status.getStatusLine().getStatusCode(), either(equalTo(200)).or(equalTo(201)));
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} finally {
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IOUtils.closeQuietly(status.getEntity().getContent());
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}
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@ -2,6 +2,7 @@ package ca.uhn.fhir.parser;
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import ca.uhn.fhir.context.ConfigurationException;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.PerformanceOptionsEnum;
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import ca.uhn.fhir.model.api.annotation.DatatypeDef;
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import ca.uhn.fhir.rest.api.Constants;
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import ca.uhn.fhir.test.BaseTest;
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@ -43,9 +44,15 @@ import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.concurrent.ExecutionException;
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import java.util.concurrent.ExecutorService;
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import java.util.concurrent.Executors;
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import java.util.concurrent.Future;
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import java.util.concurrent.TimeUnit;
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import static org.hamcrest.MatcherAssert.assertThat;
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@ -270,6 +277,50 @@ public class JsonParserR4Test extends BaseTest {
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}
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/**
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* Make sure we can perform parallel parse/encodes against the same
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* FhirContext instance when deferred model scanning is enabled without
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* running into threading issues.
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*/
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@Test
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public void testEncodeAndDecodeMultithreadedWithDeferredModelScanning() throws IOException, ExecutionException, InterruptedException {
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String input = loadResource("/multi-thread-parsing-issue-bundle.json");
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ExecutorService executor = Executors.newFixedThreadPool(10);
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for (int pass = 0; pass < 10; pass++) {
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ourLog.info("Starting pass: {}", pass);
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FhirContext parseCtx = FhirContext.forR4();
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parseCtx.setPerformanceOptions(PerformanceOptionsEnum.DEFERRED_MODEL_SCANNING);
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List<Future<Bundle>> bundleFutures = new ArrayList<>();
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for (int readIdx = 0; readIdx < 10; readIdx++) {
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bundleFutures.add(executor.submit(()->parseCtx.newJsonParser().parseResource(Bundle.class, input)));
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}
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List<Bundle> parsedBundles = new ArrayList<>();
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for (Future<Bundle> nextFuture : bundleFutures) {
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Bundle nextBundle = nextFuture.get();
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parsedBundles.add(nextBundle);
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}
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FhirContext encodeCtx = FhirContext.forR4();
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encodeCtx.setPerformanceOptions(PerformanceOptionsEnum.DEFERRED_MODEL_SCANNING);
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List<Future<String>> encodeFutures = new ArrayList<>();
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for (Bundle nextBundle : parsedBundles) {
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encodeFutures.add(executor.submit(()->encodeCtx.newJsonParser().encodeResourceToString(nextBundle)));
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}
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List<String> outputs = new ArrayList<>();
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for (Future<String> nextFuture : encodeFutures) {
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outputs.add(nextFuture.get());
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}
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assertEquals(outputs.get(0), outputs.get(1));
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}
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}
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@Test
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public void testEncodeAndParseUnicodeCharacterInNarrative() {
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Patient p = new Patient();
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@ -0,0 +1,471 @@
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{
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"resourceType": "Bundle",
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"type": "transaction",
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"entry": [
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{
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"fullUrl": "5b6a6591-ae0f-3bfc-987e-5f144a43a036",
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"resource": {
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"resourceType": "Condition",
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"id": "5b6a6591-ae0f-3bfc-987e-5f144a43a036",
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"meta": {
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"profile": [
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"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition"
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]
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},
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"identifier": [
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{
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"system": "http://bluecrossnc.com/fhir/conditionIdentifier",
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"value": "13028683"
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}
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],
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"clinicalStatus": {
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
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"code": "active"
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}
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]
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},
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"verificationStatus": {
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status",
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"code": "unconfirmed"
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}
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]
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},
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"category": [
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{
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/condition-category",
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"code": "encounter-diagnosis"
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}
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]
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}
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],
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"code": {
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"coding": [
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{
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"system": "http://hl7.org/fhir/sid/icd-10-cm",
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"code": "Z80.3"
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}
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]
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},
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"subject": {
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"reference": "Patient?_type=http://terminology.hl7.org/CodeSystem/v2-0203|MB&identifier=111111111",
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"identifier": {
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"type": {
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
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"code": "MB"
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}
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]
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},
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"value": "111111111"
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}
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}
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},
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"request": {
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"method": "PUT",
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"url": "Condition/5b6a6591-ae0f-3bfc-987e-5f144a43a036"
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}
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},
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{
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"fullUrl": "a621019a-fadb-37dd-964a-01c21926e9b4",
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"resource": {
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"resourceType": "Practitioner",
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"id": "a621019a-fadb-37dd-964a-01c21926e9b4",
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"meta": {
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"profile": [
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"http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner",
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"http://hl7.org/fhir/us/carin-bb/StructureDefinition/C4BB-Practitioner"
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]
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},
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"identifier": [
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{
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"type": {
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"coding": [
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{
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"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBIdentifierType",
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"code": "npi"
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}
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]
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},
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"system": "http://hl7.org/fhir/sid/us-npi",
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"value": "1134567787"
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}
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],
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"active": true,
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"name": [
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{
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"family": "BRIMMAGE",
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"given": [
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"BRAIN BRIMMAGE"
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]
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}
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]
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},
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"request": {
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"method": "PUT",
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"url": "Practitioner/a621019a-fadb-37dd-964a-01c21926e9b4"
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}
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},
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{
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"fullUrl": "fb1490ab-c62e-33ca-8414-b6437b0fa578",
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"resource": {
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"resourceType": "Practitioner",
|
||||
"id": "fb1490ab-c62e-33ca-8414-b6437b0fa578",
|
||||
"meta": {
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||||
"profile": [
|
||||
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner",
|
||||
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|
||||
]
|
||||
},
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||||
"identifier": [
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||||
{
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||||
"type": {
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||||
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||||
{
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||||
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|
||||
"code": "npi"
|
||||
}
|
||||
]
|
||||
},
|
||||
"system": "http://hl7.org/fhir/sid/us-npi",
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||||
"value": "1386735827"
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||||
}
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||||
],
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||||
"active": true,
|
||||
"name": [
|
||||
{
|
||||
"family": "NIEVES-ARRIBA",
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||||
"given": [
|
||||
"NIEVES-ARRIBA, LUCYBETH"
|
||||
]
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||||
}
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||||
]
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||||
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||||
"request": {
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||||
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||||
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||||
}
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||||
},
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||||
{
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||||
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||||
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||||
"name": "LabCorp",
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||||
"address": {
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||||
"line": [
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||||
"231 MAPLE AVENUE",
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||||
"BURLINGTON"
|
||||
],
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||||
"city": "NC",
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||||
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||||
}
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||||
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||||
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}
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||||
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||||
{
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"resource": {
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"resourceType": "Encounter",
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||||
"meta": {
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||||
]
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||||
},
|
||||
"identifier": [
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||||
{
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||||
"system": "http://bluecrossnc.com/fhir/encounterIdentifier",
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||||
"value": "13028683"
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||||
}
|
||||
],
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||||
"status": "finished",
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||||
"code": "AMB"
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||||
},
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||||
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||||
{
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||||
"text": "Authorization"
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||||
},
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||||
{
|
||||
"coding": [
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||||
{
|
||||
"system": "http://www.ama-assn.org/go/cpt",
|
||||
"code": "81163"
|
||||
}
|
||||
]
|
||||
}
|
||||
],
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||||
"subject": {
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||||
"reference": "Patient?_type=http://terminology.hl7.org/CodeSystem/v2-0203|MB&identifier=111111111",
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||||
"identifier": {
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||||
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||||
{
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||||
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||||
"code": "MB"
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||||
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|
||||
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||||
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|
||||
"value": "111111111"
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
{
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||||
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||||
"code": "PART"
|
||||
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||||
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||||
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||||
],
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||||
"period": {
|
||||
"start": "2021-08-27",
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||||
"end": "2021-09-26"
|
||||
},
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||||
"individual": {
|
||||
"reference": "Practitioner/a621019a-fadb-37dd-964a-01c21926e9b4"
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||||
}
|
||||
},
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||||
{
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||||
"type": [
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||||
{
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||||
"coding": [
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||||
{
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||||
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||||
"code": "PART"
|
||||
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|
||||
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|
||||
}
|
||||
],
|
||||
"period": {
|
||||
"start": "2019-04-15",
|
||||
"end": "2019-05-15"
|
||||
},
|
||||
"individual": {
|
||||
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||||
}
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||||
}
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||||
],
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||||
"period": {
|
||||
"start": "2019-04-15",
|
||||
"end": "2019-05-15"
|
||||
},
|
||||
"reasonCode": [
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||||
{
|
||||
"text": "Diagnostic Medical"
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||||
}
|
||||
],
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
"request": {
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||||
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||||
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||||
},
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{
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||||
"fullUrl": "aa00fd16-222f-36e6-ad0d-df8cf9abb325",
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||||
"resource": {
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||||
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||||
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||||
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||||
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||||
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||||
},
|
||||
"identifier": [
|
||||
{
|
||||
"system": "http://bluecrossnc.com/fhir/documentreferenceIdentifier",
|
||||
"value": "127598"
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||||
}
|
||||
],
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||||
"status": "current",
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||||
"type": {
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||||
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||||
{
|
||||
"system": "http://loinc.org",
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||||
"code": "11506-3"
|
||||
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||||
]
|
||||
},
|
||||
"category": [
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||||
{
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||||
"coding": [
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||||
{
|
||||
"system": "http://hl7.org/fhir/us/core/CodeSystem/us-core-documentreference-category",
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||||
"code": "clinical-note"
|
||||
}
|
||||
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||||
}
|
||||
],
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||||
"subject": {
|
||||
"reference": "Patient?_type=http://terminology.hl7.org/CodeSystem/v2-0203|MB&identifier=10215619000",
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
"date": "2021-09-16T20:00:00.000-04:00",
|
||||
"author": [
|
||||
{
|
||||
"reference": "Organization/BCBSNC"
|
||||
}
|
||||
],
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||||
"content": [
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||||
{
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||||
"attachment": {
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||||
"contentType": "text/plain",
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||||
"data": "VkdWemRDQlFhSGx6YVdOcFlXNGdVbUYwYVc5dVlXeGw="
|
||||
}
|
||||
}
|
||||
],
|
||||
"context": {
|
||||
"encounter": [
|
||||
{
|
||||
"display": "13028683"
|
||||
}
|
||||
],
|
||||
"period": {
|
||||
"start": "2021-08-26T20:00:00-04:00",
|
||||
"end": "2021-09-25T20:00:00-04:00"
|
||||
}
|
||||
}
|
||||
},
|
||||
"request": {
|
||||
"method": "PUT",
|
||||
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||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "89a97fee-729a-3953-9482-caeb82ee8db5",
|
||||
"resource": {
|
||||
"resourceType": "Provenance",
|
||||
"id": "89a97fee-729a-3953-9482-caeb82ee8db5",
|
||||
"meta": {
|
||||
"profile": [
|
||||
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|
||||
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|
||||
},
|
||||
"target": [
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||||
{
|
||||
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||||
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||||
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||||
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{
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
{
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||||
"reference": "Condition/5b6a6591-ae0f-3bfc-987e-5f144a43a036"
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||||
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|
||||
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||||
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||||
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||||
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||||
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|
||||
"agent": [
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||||
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||||
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||||
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||||
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||||
"code": "author"
|
||||
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||||
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||||
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||||
"who": {
|
||||
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|
||||
}
|
||||
}
|
||||
]
|
||||
},
|
||||
"request": {
|
||||
"method": "PUT",
|
||||
"url": "Provenance/89a97fee-729a-3953-9482-caeb82ee8db5"
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||||
}
|
||||
},
|
||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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||||
"target": [
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
"value": "10215619000"
|
||||
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|
||||
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|
||||
{
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"agent": [
|
||||
{
|
||||
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|
||||
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{
|
||||
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|
||||
"code": "author"
|
||||
}
|
||||
]
|
||||
},
|
||||
"who": {
|
||||
"reference": "Organization/BCBSNC"
|
||||
}
|
||||
}
|
||||
]
|
||||
},
|
||||
"request": {
|
||||
"method": "PUT",
|
||||
"url": "Provenance/69d1f8f0-87e6-3cff-bd41-c3e01a5c479d"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
Loading…
Reference in New Issue