JsonParser contained working

hapi-fhir-base/TODO.txt

@@ -33,15 +33,11 @@
  
  * Support "Binary" resource, which is a special resource type
  
- * Submit "_pretty" as possible parameter to HL7
- 
 ---------
 Issues:
  * Need to be able to bind Identifier.system to a set of allowable values in a profile. Graeme
    has suggested making value[x] repeatable in the profile definition
    
- * CarePlan.Activity has a type of "xmlIdRef" which is a weird datatype. The example here:
-   http://www.hl7.org/implement/standards/fhir/careplan-example-integrated.xml.html
-   seems to use an extension to model that element instead of the goal type too.
-   
  * Would like a standardized (but optional) HTTP parameter for pretty-printing. Suggest: _pretty=true
+ 
+ * Example-patient-general.xml/json has <reference value="Organization/1"/> but "resource":"Organization/1"

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

@@ -56,6 +56,7 @@ public class RuntimeChildUndeclaredExtensionDefinition extends BaseRuntimeChildD
 				if (!((IRuntimeDatatypeDefinition) next).isSpecialization()) {
 					String attrName = "value" + next.getName().substring(0, 1).toUpperCase() + next.getName().substring(1);
 					datatypeAttributeNameToDefinition.put(attrName, next);
+					datatypeAttributeNameToDefinition.put(attrName.toLowerCase(), next);
 				}
 			}
 		}

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java

@@ -9,10 +9,13 @@ import java.io.StringWriter;
 import java.io.Writer;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 
 import javax.json.Json;
+import javax.json.JsonArray;
 import javax.json.JsonObject;
 import javax.json.JsonReader;
 import javax.json.JsonString;
@@ -20,7 +23,6 @@ import javax.json.JsonValue;
 import javax.json.JsonValue.ValueType;
 import javax.json.stream.JsonGenerator;
 import javax.json.stream.JsonGeneratorFactory;
-import javax.json.stream.JsonParser.Event;
 
 import org.apache.commons.lang3.StringUtils;
 
@@ -45,6 +47,7 @@ import ca.uhn.fhir.model.dstu.composite.ContainedDt;
 import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.primitive.BooleanDt;
 import ca.uhn.fhir.model.primitive.DecimalDt;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.IntegerDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.model.primitive.XhtmlDt;
@@ -164,45 +167,168 @@ public class JsonParser extends BaseParser implements IParser {
 		assertObjectOfType(resourceTypeObj, JsonValue.ValueType.STRING, "resourceType");
 		String resourceType = ((JsonString) resourceTypeObj).getString();
 
+		RuntimeResourceDefinition def;
 		if (theResourceType != null) {
-			RuntimeResourceDefinition def = myContext.getResourceDefinition(theResourceType);
+			def = myContext.getResourceDefinition(theResourceType);
 		} else {
-			RuntimeResourceDefinition def = myContext.getResourceDefinition(resourceType);
+			def = myContext.getResourceDefinition(resourceType);
 		}
 
-		PushbackJsonParser parser = new PushbackJsonParser(Json.createParser(theReader));
+		ParserState<? extends IResource> state = ParserState.getPreResourceInstance(def.getImplementingClass(), myContext, true);
+		state.enteringNewElement(null, def.getName());
 
-		while (parser.hasNext()) {
+		parseChildren(object, state);
 
-			Event next = parser.next();
+		state.endingElement(null);
-			switch (next) {
+
-			case END_ARRAY:
+		@SuppressWarnings("unchecked")
+		T retVal = (T) state.getObject();
+
+		return retVal;
+	}
+
+	private void parseChildren(JsonObject theObject, ParserState<? extends IResource> theState) {
+		String elementId = null;
+		for (String nextName : theObject.keySet()) {
+			if ("resourceType".equals(nextName)) {
+				continue;
+			} else if ("id".equals(nextName)) {
+				elementId = theObject.getString(nextName);
+				continue;
+			} else if ("extension".equals(nextName)) {
+				JsonArray array = theObject.getJsonArray(nextName);
+				parseExtension(theState, array, false);
+				continue;
+			} else if ("modifierExtension".equals(nextName)) {
+				JsonArray array = theObject.getJsonArray(nextName);
+				parseExtension(theState, array, true);
+				continue;
+			} else if (nextName.charAt(0) == '_') {
+				continue;
+			}
+
+			JsonValue nextVal = theObject.get(nextName);
+			JsonValue alternateVal = theObject.get('_' + nextName);
+
+			parseChildren(theState, nextName, nextVal, alternateVal);
+
+		}
+
+		if (elementId != null) {
+			// System.out.checkError(); // TODO: remove
+			IResource object = theState.getObject();
+			object.setId(new IdDt(elementId));
+		}
+	}
+
+	private void parseChildren(ParserState<? extends IResource> theState, String theName, JsonValue theJsonVal, JsonValue theAlternateVal) {
+		switch (theJsonVal.getValueType()) {
+		case ARRAY: {
+			JsonArray nextArray = (JsonArray) theJsonVal;
+			JsonArray nextAlternateArray = (JsonArray) theAlternateVal;
+			for (int i = 0; i < nextArray.size(); i++) {
+				JsonValue nextObject = nextArray.get(i);
+				JsonValue nextAlternate = null;
+				if (nextAlternateArray != null) {
+					nextAlternate = nextAlternateArray.get(i);
+				}
+				parseChildren(theState, theName, nextObject, nextAlternate);
+			}
 			break;
-			case END_OBJECT:
+		}
+		case OBJECT: {
+			theState.enteringNewElement(null, theName);
+			JsonObject nextObject = (JsonObject) theJsonVal;
+			boolean preResource = false;
+			if (theState.isPreResource()) {
+				String resType = nextObject.getString("resourceType");
+				if (isBlank(resType)) {
+					throw new DataFormatException("Missing 'resourceType' from resource");
+				}
+				theState.enteringNewElement(null, resType);
+				preResource = true;
+			}
+			parseChildren(nextObject, theState);
+			if (preResource) {
+				theState.endingElement(null);
+			}
+			theState.endingElement(null);
 			break;
-			case KEY_NAME:
+		}
+		case STRING: {
+			JsonString nextValStr = (JsonString) theJsonVal;
+			theState.enteringNewElement(null, theName);
+			theState.attributeValue("value", nextValStr.getString());
+			parseAlternates(theAlternateVal, theState);
+			theState.endingElement(null);
 			break;
-			case START_ARRAY:
+		}
+		case NUMBER:
+		case FALSE:
+		case TRUE:
+			theState.enteringNewElement(null, theName);
+			theState.attributeValue("value", theJsonVal.toString());
+			parseAlternates(theAlternateVal, theState);
+			theState.endingElement(null);
 			break;
-			case START_OBJECT:
+		case NULL:
 			break;
-			case VALUE_FALSE:
+		}
-			case VALUE_TRUE:
+	}
+
+	private void parseAlternates(JsonValue theAlternateVal, ParserState<? extends IResource> theState) {
+		if (theAlternateVal == null || theAlternateVal.getValueType() == ValueType.NULL) {
+			return;
+		}
+		JsonObject alternate = (JsonObject) theAlternateVal;
+		for (Entry<String, JsonValue> nextEntry : alternate.entrySet()) {
+			String nextKey = nextEntry.getKey();
+			JsonValue nextVal = nextEntry.getValue();
+			if ("extension".equals(nextKey)) {
+				boolean isModifier = false;
+				JsonArray array = (JsonArray) nextEntry.getValue();
+				parseExtension(theState, array, isModifier);
+			} else if ("modifierExtension".equals(nextKey)) {
+				boolean isModifier = true;
+				JsonArray array = (JsonArray) nextEntry.getValue();
+				parseExtension(theState, array, isModifier);
+			} else if ("id".equals(nextKey)) {
+				switch (nextVal.getValueType()) {
+				case STRING:
+					theState.attributeValue("id", ((JsonString) nextVal).getString());
 					break;
-			case VALUE_NULL:
+				case NULL:
-				break;
-			case VALUE_NUMBER:
-				break;
-			case VALUE_STRING:
 					break;
 				default:
 					break;
-
+				}
+			}
+		}
 	}
 
+	private void parseExtension(ParserState<? extends IResource> theState, JsonArray array, boolean theIsModifier) {
+		// TODO: use theIsModifier
+		for (int i = 0; i < array.size(); i++) {
+			JsonObject nextExtObj = array.getJsonObject(i);
+			String url = nextExtObj.getString("url");
+			theState.enteringNewElementExtension(null, url, false);
+			for (Iterator<String> iter = nextExtObj.keySet().iterator(); iter.hasNext();) {
+				String next = iter.next();
+				if ("url".equals(next)) {
+					continue;
+				} else if ("extension".equals(next)) {
+					JsonArray jsonVal = (JsonArray) nextExtObj.get(next);
+					parseExtension(theState, jsonVal, false);
+				} else if ("modifierExtension".equals(next)) {
+					JsonArray jsonVal = (JsonArray) nextExtObj.get(next);
+					parseExtension(theState, jsonVal, true);
+				} else {
+					JsonValue jsonVal = nextExtObj.get(next);
+					parseChildren(theState, next, jsonVal, null);
+				}
+			}
+			theState.endingElement(null);
 		}
-
-		return null;
 	}
 
 	@Override

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

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.parser;
 
-
 import static org.apache.commons.lang3.StringUtils.*;
 
 import java.util.ArrayList;
@@ -49,9 +48,11 @@ class ParserState<T extends IElement> {
 	private FhirContext myContext;
 	private T myObject;
 	private BaseState myState;
+	private boolean myJsonMode;
 
-	private ParserState(FhirContext theContext) {
+	private ParserState(FhirContext theContext, boolean theJsonMode) {
 		myContext = theContext;
+		myJsonMode = theJsonMode;
 	}
 
 	public void attributeValue(String theName, String theValue) throws DataFormatException {
@@ -70,8 +71,9 @@ class ParserState<T extends IElement> {
 		myState.enteringNewElementExtension(theElem, theUrlAttr, theIsModifier);
 	}
 
+	@SuppressWarnings("unchecked")
 	public T getObject() {
-		return myObject;
+		return (T) myState.getCurrentElement();
 	}
 
 	public boolean isComplete() {
@@ -105,8 +107,8 @@ class ParserState<T extends IElement> {
 		myState = theState;
 	}
 
-	public static ParserState<Bundle> getPreAtomInstance(FhirContext theContext) throws DataFormatException {
+	public static ParserState<Bundle> getPreAtomInstance(FhirContext theContext, boolean theJsonMode) throws DataFormatException {
-		ParserState<Bundle> retVal = new ParserState<Bundle>(theContext);
+		ParserState<Bundle> retVal = new ParserState<Bundle>(theContext, theJsonMode);
 		retVal.push(retVal.new PreAtomState());
 		return retVal;
 	}
@@ -115,8 +117,8 @@ class ParserState<T extends IElement> {
 	 * @param theResourceType
 	 *            May be null
 	 */
-	public static <T extends IResource> ParserState<T> getPreResourceInstance(Class<T> theResourceType, FhirContext theContext) throws DataFormatException {
+	public static <T extends IResource> ParserState<T> getPreResourceInstance(Class<T> theResourceType, FhirContext theContext, boolean theJsonMode) throws DataFormatException {
-		ParserState<T> retVal = new ParserState<T>(theContext);
+		ParserState<T> retVal = new ParserState<T>(theContext, theJsonMode);
 		retVal.push(retVal.new PreResourceState(theResourceType));
 		return retVal;
 	}
@@ -212,7 +214,7 @@ class ParserState<T extends IElement> {
 			} else if ("content".equals(theLocalPart)) {
 				push(new PreResourceState(myEntry));
 			} else if ("summary".equals(theLocalPart)) {
-				push(new XhtmlState(getPreResourceState(),myEntry.getSummary(), false));
+				push(new XhtmlState(getPreResourceState(), myEntry.getSummary(), false));
 			} else if ("category".equals(theLocalPart)) {
 				push(new AtomCategoryState(myEntry.addCategory()));
 			} else {
@@ -433,10 +435,13 @@ class ParserState<T extends IElement> {
 			return null;
 		}
 
+		public boolean isPreResource() {
+			return false;
 		}
 
-	private class ContainedResourcesState extends PreResourceState
+	}
-	{
+
+	private class ContainedResourcesState extends PreResourceState {
 
 		public ContainedResourcesState(PreResourceState thePreResourcesState) {
 			super(thePreResourcesState);
@@ -451,7 +456,7 @@ class ParserState<T extends IElement> {
 		public void wereBack() {
 			IResource res = getCurrentElement();
 			assert res != null;
-			if (res.getId()==null || res.getId().isEmpty()) {
+			if (res.getId() == null || res.getId().isEmpty()) {
 				ourLog.debug("Discarding contained resource with no ID!");
 			} else {
 				getPreResourceState().getContainedResources().put(res.getId().getValueAsString(), res);
@@ -459,7 +464,6 @@ class ParserState<T extends IElement> {
 			getPreResourceState().getCurrentElement().getContained().getContainedResources().add(res);
 		}
 
-		
 	}
 
 	private class DeclaredExtensionState extends BaseState {
@@ -471,7 +475,7 @@ class ParserState<T extends IElement> {
 
 		public DeclaredExtensionState(PreResourceState thePreResourceState, RuntimeChildDeclaredExtensionDefinition theDefinition, IElement theParentInstance) {
 			super(thePreResourceState);
-			myPreResourceState=thePreResourceState;
+			myPreResourceState = thePreResourceState;
 			myDefinition = theDefinition;
 			myParentInstance = theParentInstance;
 		}
@@ -625,8 +629,14 @@ class ParserState<T extends IElement> {
 			}
 			case CONTAINED_RESOURCES: {
 				RuntimeElemContainedResources targetElem = (RuntimeElemContainedResources) target;
-				ContainedDt newDt = targetElem.newInstance();
+				List<? extends IElement> values = child.getAccessor().getValues(myInstance);
+				ContainedDt newDt;
+				if (values == null || values.isEmpty() || values.get(0) == null) {
+					newDt = targetElem.newInstance();
 					child.getMutator().addValue(myInstance, newDt);
+				}else {
+					newDt = (ContainedDt) values.get(0);
+				}
 				ContainedResourcesState state = new ContainedResourcesState(getPreResourceState());
 				push(state);
 				return;
@@ -723,7 +733,6 @@ class ParserState<T extends IElement> {
 
 	}
 
-	
 	private class PreAtomState extends BaseState {
 
 		private Bundle myInstance;
@@ -771,6 +780,11 @@ class ParserState<T extends IElement> {
 
 		private Class<? extends IResource> myResourceType;
 
+		@Override
+		public boolean isPreResource() {
+			return true;
+		}
+
 		public PreResourceState(BundleEntry theEntry) {
 			super(null);
 			myEntry = theEntry;
@@ -835,7 +849,7 @@ class ParserState<T extends IElement> {
 
 			for (ResourceReferenceDt nextRef : myResourceReferences) {
 				String ref = nextRef.getReference().getValue();
-				if (isNotBlank(ref)){
+				if (isNotBlank(ref)) {
 					if (ref.startsWith("#")) {
 						IResource target = myContainedResources.get(ref.substring(1));
 						if (target != null) {
@@ -868,6 +882,8 @@ class ParserState<T extends IElement> {
 		public void attributeValue(String theName, String theValue) throws DataFormatException {
 			if ("value".equals(theName)) {
 				myInstance.setValueAsString(theValue);
+			} else if ("id".equals(theName)) {
+				myInstance.setId(new IdDt(theValue));
 			}
 		}
 
@@ -889,7 +905,10 @@ class ParserState<T extends IElement> {
 
 		@Override
 		public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
-			throw new Error("?? can this happen?"); // TODO: can this happen?
+			throw new Error("Element " + theLocalPart + " in primitive!"); // TODO:
+																			// can
+																			// this
+																			// happen?
 		}
 
 		@Override
@@ -952,6 +971,9 @@ class ParserState<T extends IElement> {
 				} else if ("reference".equals(theLocalPart)) {
 					mySubState = ResourceReferenceSubState.REFERENCE;
 					break;
+				} else if ("resource".equals(theLocalPart)) {
+					mySubState = ResourceReferenceSubState.REFERENCE;
+					break;
 				}
 				//$FALL-THROUGH$
 			case DISPLAY:
@@ -971,7 +993,6 @@ class ParserState<T extends IElement> {
 		DISPLAY, INITIAL, REFERENCE
 	}
 
-
 	private class XhtmlState extends BaseState {
 		private int myDepth;
 		private XhtmlDt myDt;
@@ -985,6 +1006,24 @@ class ParserState<T extends IElement> {
 			myIncludeOuterEvent = theIncludeOuterEvent;
 		}
 
+		@Override
+		public void attributeValue(String theName, String theValue) throws DataFormatException {
+			if (myJsonMode) {
+				myDt.setValueAsString(theValue);
+				return;
+			}
+			super.attributeValue(theName, theValue);
+		}
+
+		@Override
+		public void endingElement(EndElement theElem) throws DataFormatException {
+			if (myJsonMode) {
+				pop();
+				return;
+			}
+			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();
+	}
+
 }

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

@@ -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);
 	}
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java

@@ -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 {
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/ResfulServerMethodTest.java

@@ -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));
 
 	}