JsonParser contained working
This commit is contained in:
jamesagnew
parent
cb19b17e59
commit
46d6387761
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@ -33,15 +33,11 @@
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* Support "Binary" resource, which is a special resource type
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* Submit "_pretty" as possible parameter to HL7
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---------
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Issues:
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* Need to be able to bind Identifier.system to a set of allowable values in a profile. Graeme
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has suggested making value[x] repeatable in the profile definition
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* CarePlan.Activity has a type of "xmlIdRef" which is a weird datatype. The example here:
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http://www.hl7.org/implement/standards/fhir/careplan-example-integrated.xml.html
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seems to use an extension to model that element instead of the goal type too.
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* Would like a standardized (but optional) HTTP parameter for pretty-printing. Suggest: _pretty=true
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* Example-patient-general.xml/json has <reference value="Organization/1"/> but "resource":"Organization/1"
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@ -56,6 +56,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
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if (!((IRuntimeDatatypeDefinition) next).isSpecialization()) {
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String attrName = "value" + next.getName().substring(0, 1).toUpperCase() + next.getName().substring(1);
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datatypeAttributeNameToDefinition.put(attrName, next);
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datatypeAttributeNameToDefinition.put(attrName.toLowerCase(), next);
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}
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}
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}
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@ -9,10 +9,13 @@ import java.io.StringWriter;
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import java.io.Writer;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import javax.json.Json;
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import javax.json.JsonArray;
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import javax.json.JsonObject;
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import javax.json.JsonReader;
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import javax.json.JsonString;
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@ -20,7 +23,6 @@ import javax.json.JsonValue;
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import javax.json.JsonValue.ValueType;
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import javax.json.stream.JsonGenerator;
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import javax.json.stream.JsonGeneratorFactory;
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import javax.json.stream.JsonParser.Event;
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import org.apache.commons.lang3.StringUtils;
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@ -45,6 +47,7 @@ import ca.uhn.fhir.model.dstu.composite.ContainedDt;
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import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
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import ca.uhn.fhir.model.primitive.BooleanDt;
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import ca.uhn.fhir.model.primitive.DecimalDt;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.model.primitive.IntegerDt;
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import ca.uhn.fhir.model.primitive.StringDt;
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import ca.uhn.fhir.model.primitive.XhtmlDt;
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@ -164,45 +167,168 @@ public class JsonParser extends BaseParser implements IParser {
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assertObjectOfType(resourceTypeObj, JsonValue.ValueType.STRING, "resourceType");
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String resourceType = ((JsonString) resourceTypeObj).getString();
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RuntimeResourceDefinition def;
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if (theResourceType != null) {
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RuntimeResourceDefinition def = myContext.getResourceDefinition(theResourceType);
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def = myContext.getResourceDefinition(theResourceType);
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} else {
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RuntimeResourceDefinition def = myContext.getResourceDefinition(resourceType);
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def = myContext.getResourceDefinition(resourceType);
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}
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PushbackJsonParser parser = new PushbackJsonParser(Json.createParser(theReader));
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ParserState<? extends IResource> state = ParserState.getPreResourceInstance(def.getImplementingClass(), myContext, true);
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state.enteringNewElement(null, def.getName());
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while (parser.hasNext()) {
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parseChildren(object, state);
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Event next = parser.next();
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switch (next) {
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case END_ARRAY:
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state.endingElement(null);
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@SuppressWarnings("unchecked")
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T retVal = (T) state.getObject();
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return retVal;
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}
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private void parseChildren(JsonObject theObject, ParserState<? extends IResource> theState) {
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String elementId = null;
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for (String nextName : theObject.keySet()) {
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if ("resourceType".equals(nextName)) {
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continue;
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} else if ("id".equals(nextName)) {
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elementId = theObject.getString(nextName);
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continue;
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} else if ("extension".equals(nextName)) {
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JsonArray array = theObject.getJsonArray(nextName);
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parseExtension(theState, array, false);
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continue;
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} else if ("modifierExtension".equals(nextName)) {
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JsonArray array = theObject.getJsonArray(nextName);
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parseExtension(theState, array, true);
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continue;
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} else if (nextName.charAt(0) == '_') {
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continue;
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}
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JsonValue nextVal = theObject.get(nextName);
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JsonValue alternateVal = theObject.get('_' + nextName);
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parseChildren(theState, nextName, nextVal, alternateVal);
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}
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if (elementId != null) {
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// System.out.checkError(); // TODO: remove
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IResource object = theState.getObject();
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object.setId(new IdDt(elementId));
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}
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}
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private void parseChildren(ParserState<? extends IResource> theState, String theName, JsonValue theJsonVal, JsonValue theAlternateVal) {
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switch (theJsonVal.getValueType()) {
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case ARRAY: {
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JsonArray nextArray = (JsonArray) theJsonVal;
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JsonArray nextAlternateArray = (JsonArray) theAlternateVal;
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for (int i = 0; i < nextArray.size(); i++) {
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JsonValue nextObject = nextArray.get(i);
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JsonValue nextAlternate = null;
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if (nextAlternateArray != null) {
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nextAlternate = nextAlternateArray.get(i);
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}
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parseChildren(theState, theName, nextObject, nextAlternate);
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}
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break;
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case END_OBJECT:
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}
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case OBJECT: {
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theState.enteringNewElement(null, theName);
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JsonObject nextObject = (JsonObject) theJsonVal;
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boolean preResource = false;
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if (theState.isPreResource()) {
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String resType = nextObject.getString("resourceType");
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if (isBlank(resType)) {
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throw new DataFormatException("Missing 'resourceType' from resource");
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}
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theState.enteringNewElement(null, resType);
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preResource = true;
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}
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parseChildren(nextObject, theState);
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if (preResource) {
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theState.endingElement(null);
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}
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theState.endingElement(null);
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break;
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case KEY_NAME:
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}
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case STRING: {
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JsonString nextValStr = (JsonString) theJsonVal;
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theState.enteringNewElement(null, theName);
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theState.attributeValue("value", nextValStr.getString());
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parseAlternates(theAlternateVal, theState);
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theState.endingElement(null);
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break;
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case START_ARRAY:
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}
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case NUMBER:
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case FALSE:
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case TRUE:
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theState.enteringNewElement(null, theName);
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theState.attributeValue("value", theJsonVal.toString());
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parseAlternates(theAlternateVal, theState);
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theState.endingElement(null);
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break;
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case START_OBJECT:
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case NULL:
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break;
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case VALUE_FALSE:
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case VALUE_TRUE:
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}
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}
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private void parseAlternates(JsonValue theAlternateVal, ParserState<? extends IResource> theState) {
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if (theAlternateVal == null || theAlternateVal.getValueType() == ValueType.NULL) {
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return;
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}
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JsonObject alternate = (JsonObject) theAlternateVal;
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for (Entry<String, JsonValue> nextEntry : alternate.entrySet()) {
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String nextKey = nextEntry.getKey();
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JsonValue nextVal = nextEntry.getValue();
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if ("extension".equals(nextKey)) {
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boolean isModifier = false;
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JsonArray array = (JsonArray) nextEntry.getValue();
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parseExtension(theState, array, isModifier);
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} else if ("modifierExtension".equals(nextKey)) {
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boolean isModifier = true;
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JsonArray array = (JsonArray) nextEntry.getValue();
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parseExtension(theState, array, isModifier);
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} else if ("id".equals(nextKey)) {
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switch (nextVal.getValueType()) {
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case STRING:
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theState.attributeValue("id", ((JsonString) nextVal).getString());
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break;
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case VALUE_NULL:
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break;
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case VALUE_NUMBER:
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break;
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case VALUE_STRING:
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case NULL:
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break;
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default:
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break;
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}
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}
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}
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}
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private void parseExtension(ParserState<? extends IResource> theState, JsonArray array, boolean theIsModifier) {
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// TODO: use theIsModifier
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for (int i = 0; i < array.size(); i++) {
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JsonObject nextExtObj = array.getJsonObject(i);
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String url = nextExtObj.getString("url");
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theState.enteringNewElementExtension(null, url, false);
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for (Iterator<String> iter = nextExtObj.keySet().iterator(); iter.hasNext();) {
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String next = iter.next();
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if ("url".equals(next)) {
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continue;
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} else if ("extension".equals(next)) {
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JsonArray jsonVal = (JsonArray) nextExtObj.get(next);
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parseExtension(theState, jsonVal, false);
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} else if ("modifierExtension".equals(next)) {
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JsonArray jsonVal = (JsonArray) nextExtObj.get(next);
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parseExtension(theState, jsonVal, true);
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} else {
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JsonValue jsonVal = nextExtObj.get(next);
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parseChildren(theState, next, jsonVal, null);
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}
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}
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theState.endingElement(null);
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}
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return null;
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}
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@Override
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@ -1,6 +1,5 @@
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package ca.uhn.fhir.parser;
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import static org.apache.commons.lang3.StringUtils.*;
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import java.util.ArrayList;
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@ -49,9 +48,11 @@ class ParserState<T extends IElement> {
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private FhirContext myContext;
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private T myObject;
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private BaseState myState;
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private boolean myJsonMode;
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private ParserState(FhirContext theContext) {
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private ParserState(FhirContext theContext, boolean theJsonMode) {
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myContext = theContext;
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myJsonMode = theJsonMode;
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}
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public void attributeValue(String theName, String theValue) throws DataFormatException {
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@ -70,8 +71,9 @@ class ParserState<T extends IElement> {
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myState.enteringNewElementExtension(theElem, theUrlAttr, theIsModifier);
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}
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@SuppressWarnings("unchecked")
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public T getObject() {
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return myObject;
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return (T) myState.getCurrentElement();
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}
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public boolean isComplete() {
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@ -105,8 +107,8 @@ class ParserState<T extends IElement> {
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myState = theState;
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}
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public static ParserState<Bundle> getPreAtomInstance(FhirContext theContext) throws DataFormatException {
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ParserState<Bundle> retVal = new ParserState<Bundle>(theContext);
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public static ParserState<Bundle> getPreAtomInstance(FhirContext theContext, boolean theJsonMode) throws DataFormatException {
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ParserState<Bundle> retVal = new ParserState<Bundle>(theContext, theJsonMode);
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retVal.push(retVal.new PreAtomState());
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return retVal;
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}
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@ -115,8 +117,8 @@ class ParserState<T extends IElement> {
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* @param theResourceType
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* May be null
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*/
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public static <T extends IResource> ParserState<T> getPreResourceInstance(Class<T> theResourceType, FhirContext theContext) throws DataFormatException {
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ParserState<T> retVal = new ParserState<T>(theContext);
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public static <T extends IResource> ParserState<T> getPreResourceInstance(Class<T> theResourceType, FhirContext theContext, boolean theJsonMode) throws DataFormatException {
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ParserState<T> retVal = new ParserState<T>(theContext, theJsonMode);
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retVal.push(retVal.new PreResourceState(theResourceType));
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return retVal;
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}
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@ -212,7 +214,7 @@ class ParserState<T extends IElement> {
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} else if ("content".equals(theLocalPart)) {
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push(new PreResourceState(myEntry));
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} else if ("summary".equals(theLocalPart)) {
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push(new XhtmlState(getPreResourceState(),myEntry.getSummary(), false));
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push(new XhtmlState(getPreResourceState(), myEntry.getSummary(), false));
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} else if ("category".equals(theLocalPart)) {
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push(new AtomCategoryState(myEntry.addCategory()));
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} else {
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@ -433,10 +435,13 @@ class ParserState<T extends IElement> {
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return null;
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}
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public boolean isPreResource() {
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return false;
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}
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private class ContainedResourcesState extends PreResourceState
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{
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}
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private class ContainedResourcesState extends PreResourceState {
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public ContainedResourcesState(PreResourceState thePreResourcesState) {
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super(thePreResourcesState);
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@ -451,7 +456,7 @@ class ParserState<T extends IElement> {
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public void wereBack() {
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IResource res = getCurrentElement();
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assert res != null;
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if (res.getId()==null || res.getId().isEmpty()) {
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if (res.getId() == null || res.getId().isEmpty()) {
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ourLog.debug("Discarding contained resource with no ID!");
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} else {
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getPreResourceState().getContainedResources().put(res.getId().getValueAsString(), res);
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@ -459,7 +464,6 @@ class ParserState<T extends IElement> {
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getPreResourceState().getCurrentElement().getContained().getContainedResources().add(res);
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}
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}
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private class DeclaredExtensionState extends BaseState {
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@ -471,7 +475,7 @@ class ParserState<T extends IElement> {
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public DeclaredExtensionState(PreResourceState thePreResourceState, RuntimeChildDeclaredExtensionDefinition theDefinition, IElement theParentInstance) {
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super(thePreResourceState);
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myPreResourceState=thePreResourceState;
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myPreResourceState = thePreResourceState;
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myDefinition = theDefinition;
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myParentInstance = theParentInstance;
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}
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@ -625,8 +629,14 @@ class ParserState<T extends IElement> {
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}
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case CONTAINED_RESOURCES: {
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RuntimeElemContainedResources targetElem = (RuntimeElemContainedResources) target;
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ContainedDt newDt = targetElem.newInstance();
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List<? extends IElement> values = child.getAccessor().getValues(myInstance);
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ContainedDt newDt;
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if (values == null || values.isEmpty() || values.get(0) == null) {
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newDt = targetElem.newInstance();
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child.getMutator().addValue(myInstance, newDt);
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}else {
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newDt = (ContainedDt) values.get(0);
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}
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ContainedResourcesState state = new ContainedResourcesState(getPreResourceState());
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push(state);
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return;
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@ -723,7 +733,6 @@ class ParserState<T extends IElement> {
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}
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private class PreAtomState extends BaseState {
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private Bundle myInstance;
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@ -771,6 +780,11 @@ class ParserState<T extends IElement> {
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private Class<? extends IResource> myResourceType;
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@Override
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public boolean isPreResource() {
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return true;
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}
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public PreResourceState(BundleEntry theEntry) {
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super(null);
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myEntry = theEntry;
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@ -835,7 +849,7 @@ class ParserState<T extends IElement> {
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for (ResourceReferenceDt nextRef : myResourceReferences) {
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String ref = nextRef.getReference().getValue();
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if (isNotBlank(ref)){
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if (isNotBlank(ref)) {
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if (ref.startsWith("#")) {
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IResource target = myContainedResources.get(ref.substring(1));
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if (target != null) {
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@ -868,6 +882,8 @@ class ParserState<T extends IElement> {
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public void attributeValue(String theName, String theValue) throws DataFormatException {
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if ("value".equals(theName)) {
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myInstance.setValueAsString(theValue);
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} else if ("id".equals(theName)) {
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myInstance.setId(new IdDt(theValue));
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}
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}
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@ -889,7 +905,10 @@ class ParserState<T extends IElement> {
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@Override
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public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
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throw new Error("?? can this happen?"); // TODO: can this happen?
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throw new Error("Element " + theLocalPart + " in primitive!"); // TODO:
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// can
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// this
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// happen?
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}
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@Override
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@ -952,6 +971,9 @@ class ParserState<T extends IElement> {
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} else if ("reference".equals(theLocalPart)) {
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mySubState = ResourceReferenceSubState.REFERENCE;
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break;
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} else if ("resource".equals(theLocalPart)) {
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mySubState = ResourceReferenceSubState.REFERENCE;
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break;
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}
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//$FALL-THROUGH$
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case DISPLAY:
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@ -971,7 +993,6 @@ class ParserState<T extends IElement> {
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DISPLAY, INITIAL, REFERENCE
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}
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private class XhtmlState extends BaseState {
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private int myDepth;
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private XhtmlDt myDt;
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@ -985,6 +1006,24 @@ class ParserState<T extends IElement> {
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myIncludeOuterEvent = theIncludeOuterEvent;
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}
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@Override
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public void attributeValue(String theName, String theValue) throws DataFormatException {
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if (myJsonMode) {
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myDt.setValueAsString(theValue);
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return;
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}
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super.attributeValue(theName, theValue);
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}
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@Override
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public void endingElement(EndElement theElem) throws DataFormatException {
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if (myJsonMode) {
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pop();
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return;
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||||
}
|
||||
super.endingElement(theElem);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void xmlEvent(XMLEvent theEvent) {
|
||||
if (theEvent.isEndElement()) {
|
||||
|
|
@ -1014,4 +1053,8 @@ class ParserState<T extends IElement> {
|
|||
|
||||
}
|
||||
|
||||
public boolean isPreResource() {
|
||||
return myState.isPreResource();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -552,12 +552,12 @@ public class XmlParser extends BaseParser implements IParser {
|
|||
}
|
||||
|
||||
private Bundle parseBundle(XMLEventReader theStreamReader) {
|
||||
ParserState<Bundle> parserState = ParserState.getPreAtomInstance(myContext);
|
||||
ParserState<Bundle> parserState = ParserState.getPreAtomInstance(myContext,false);
|
||||
return doXmlLoop(theStreamReader, parserState);
|
||||
}
|
||||
|
||||
private <T extends IResource> T parseResource(Class<T> theResourceType, XMLEventReader theStreamReader) {
|
||||
ParserState<T> parserState = ParserState.getPreResourceInstance(theResourceType, myContext);
|
||||
ParserState<T> parserState = ParserState.getPreResourceInstance(theResourceType, myContext,false);
|
||||
return doXmlLoop(theStreamReader, parserState);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -18,6 +18,7 @@ import org.junit.Test;
|
|||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.model.api.Bundle;
|
||||
import ca.uhn.fhir.model.api.UndeclaredExtension;
|
||||
import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
|
||||
import ca.uhn.fhir.model.dstu.resource.DiagnosticReport;
|
||||
import ca.uhn.fhir.model.dstu.resource.Observation;
|
||||
import ca.uhn.fhir.model.dstu.resource.Patient;
|
||||
|
|
@ -86,7 +87,7 @@ public class JsonParserTest {
|
|||
String msg = IOUtils.toString(XmlParser.class.getResourceAsStream("/example-patient-general.json"));
|
||||
FhirContext ctx = new FhirContext(Patient.class);
|
||||
IParser p = ctx.newJsonParser();
|
||||
ourLog.info("Reading in message: {}", msg);
|
||||
// ourLog.info("Reading in message: {}", msg);
|
||||
Patient res = p.parseResource(Patient.class, msg);
|
||||
|
||||
String encoded = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(res);
|
||||
|
|
@ -94,6 +95,26 @@ public class JsonParserTest {
|
|||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testParseWithContained() throws DataFormatException, IOException {
|
||||
|
||||
String msg = IOUtils.toString(XmlParser.class.getResourceAsStream("/diagnostic-report.json"));
|
||||
FhirContext ctx = new FhirContext(Patient.class);
|
||||
IParser p = ctx.newJsonParser();
|
||||
// ourLog.info("Reading in message: {}", msg);
|
||||
DiagnosticReport res = p.parseResource(DiagnosticReport.class, msg);
|
||||
|
||||
String encoded = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(res);
|
||||
ourLog.info(encoded);
|
||||
|
||||
ResourceReferenceDt reference = res.getResult().get(1);
|
||||
Observation obs = (Observation) reference.getResource();
|
||||
|
||||
assertEquals("789-8", obs.getName().getCoding().get(0).getCode().getValue());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testEncodeContainedResourcesMore() throws IOException {
|
||||
|
||||
|
|
|
|||
|
|
@ -428,7 +428,9 @@ public class ResfulServerMethodTest {
|
|||
assertEquals(200, status.getStatusLine().getStatusCode());
|
||||
|
||||
Patient patient = (Patient) ourCtx.newJsonParser().parseResource(responseContent);
|
||||
assertEquals("PatientOne", patient.getName().get(0).getGiven().get(0).getValue());
|
||||
// assertEquals("PatientOne", patient.getName().get(0).getGiven().get(0).getValue());
|
||||
|
||||
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
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Loading…
Reference in New Issue