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org.hl7.fhir.dstu3.elementmodel.JsonParser Maven / Gradle / Ivy
package org.hl7.fhir.dstu3.elementmodel;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.UnsupportedEncodingException;
import java.math.BigDecimal;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import org.hl7.fhir.dstu3.context.IWorkerContext;
import org.hl7.fhir.dstu3.elementmodel.Element.SpecialElement;
import org.hl7.fhir.dstu3.formats.IParser.OutputStyle;
import org.hl7.fhir.dstu3.formats.JsonCreator;
import org.hl7.fhir.dstu3.formats.JsonCreatorCanonical;
import org.hl7.fhir.dstu3.formats.JsonCreatorGson;
import org.hl7.fhir.dstu3.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.utils.formats.JsonTrackingParser;
import org.hl7.fhir.dstu3.utils.formats.JsonTrackingParser.LocationData;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.xhtml.XhtmlParser;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonNull;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
public class JsonParser extends ParserBase {
private JsonCreator json;
private Map map;
public JsonParser(IWorkerContext context) {
super(context);
}
public Element parse(String source, String type) throws Exception {
JsonObject obj = (JsonObject) new com.google.gson.JsonParser().parse(source);
String path = "/"+type;
StructureDefinition sd = getDefinition(-1, -1, type);
if (sd == null)
return null;
Element result = new Element(type, new Property(context, sd.getSnapshot().getElement().get(0), sd));
checkObject(obj, path);
result.setType(type);
parseChildren(path, obj, result, true);
result.numberChildren();
return result;
}
@Override
public Element parse(InputStream stream) throws IOException, FHIRFormatError, DefinitionException {
// if we're parsing at this point, then we're going to use the custom parser
map = new HashMap();
String source = TextFile.streamToString(stream);
if (policy == ValidationPolicy.EVERYTHING) {
JsonObject obj = null;
try {
obj = JsonTrackingParser.parse(source, map);
} catch (Exception e) {
logError(-1, -1, "(document)", IssueType.INVALID, "Error parsing JSON: "+e.getMessage(), IssueSeverity.FATAL);
return null;
}
assert (map.containsKey(obj));
return parse(obj);
} else {
JsonObject obj = (JsonObject) new com.google.gson.JsonParser().parse(source);
// assert (map.containsKey(obj));
return parse(obj);
}
}
public Element parse(JsonObject object, Map map) throws FHIRFormatError, DefinitionException {
this.map = map;
return parse(object);
}
public Element parse(JsonObject object) throws FHIRFormatError, DefinitionException {
JsonElement rt = object.get("resourceType");
if (rt == null) {
logError(line(object), col(object), "$", IssueType.INVALID, "Unable to find resourceType property", IssueSeverity.FATAL);
return null;
} else {
String name = rt.getAsString();
String path = "/"+name;
StructureDefinition sd = getDefinition(line(object), col(object), name);
if (sd == null)
return null;
Element result = new Element(name, new Property(context, sd.getSnapshot().getElement().get(0), sd));
checkObject(object, path);
result.markLocation(line(object), col(object));
result.setType(name);
parseChildren(path, object, result, true);
result.numberChildren();
return result;
}
}
private void checkObject(JsonObject object, String path) throws FHIRFormatError {
if (policy == ValidationPolicy.EVERYTHING) {
boolean found = false;
for (Entry e : object.entrySet()) {
// if (!e.getKey().equals("fhir_comments")) {
found = true;
break;
// }
}
if (!found)
logError(line(object), col(object), path, IssueType.INVALID, "Object must have some content", IssueSeverity.ERROR);
}
}
private void parseChildren(String path, JsonObject object, Element context, boolean hasResourceType) throws DefinitionException, FHIRFormatError {
reapComments(object, context);
List properties = context.getProperty().getChildProperties(context.getName(), null);
Set processed = new HashSet();
if (hasResourceType)
processed.add("resourceType");
processed.add("fhir_comments");
// note that we do not trouble ourselves to maintain the wire format order here - we don't even know what it was anyway
// first pass: process the properties
for (Property property : properties) {
if (property.isChoice()) {
for (TypeRefComponent type : property.getDefinition().getType()) {
String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getCode());
if (!isPrimitive(type.getCode()) && object.has(eName)) {
parseChildComplex(path, object, context, processed, property, eName);
break;
} else if (isPrimitive(type.getCode()) && (object.has(eName) || object.has("_"+eName))) {
parseChildPrimitive(object, context, processed, property, path, eName);
break;
}
}
} else if (property.isPrimitive(property.getType(null))) {
parseChildPrimitive(object, context, processed, property, path, property.getName());
} else if (object.has(property.getName())) {
parseChildComplex(path, object, context, processed, property, property.getName());
}
}
// second pass: check for things not processed
if (policy != ValidationPolicy.NONE) {
for (Entry e : object.entrySet()) {
if (!processed.contains(e.getKey())) {
logError(line(e.getValue()), col(e.getValue()), path, IssueType.STRUCTURE, "Unrecognised property '@"+e.getKey()+"'", IssueSeverity.ERROR);
}
}
}
}
private void parseChildComplex(String path, JsonObject object, Element context, Set processed, Property property, String name) throws FHIRFormatError, DefinitionException {
processed.add(name);
String npath = path+"/"+property.getName();
JsonElement e = object.get(name);
if (property.isList() && (e instanceof JsonArray)) {
JsonArray arr = (JsonArray) e;
for (JsonElement am : arr) {
parseChildComplexInstance(npath, object, context, property, name, am);
}
} else {
parseChildComplexInstance(npath, object, context, property, name, e);
}
}
private void parseChildComplexInstance(String npath, JsonObject object, Element context, Property property, String name, JsonElement e) throws FHIRFormatError, DefinitionException {
if (e instanceof JsonObject) {
JsonObject child = (JsonObject) e;
Element n = new Element(name, property).markLocation(line(child), col(child));
checkObject(child, npath);
context.getChildren().add(n);
if (property.isResource())
parseResource(npath, child, n, property);
else
parseChildren(npath, child, n, false);
} else
logError(line(e), col(e), npath, IssueType.INVALID, "This property must be "+(property.isList() ? "an Array" : "an Object")+", not a "+e.getClass().getName(), IssueSeverity.ERROR);
}
private void parseChildPrimitive(JsonObject object, Element context, Set processed, Property property, String path, String name) throws FHIRFormatError, DefinitionException {
String npath = path+"/"+property.getName();
processed.add(name);
processed.add("_"+name);
JsonElement main = object.has(name) ? object.get(name) : null;
JsonElement fork = object.has("_"+name) ? object.get("_"+name) : null;
if (main != null || fork != null) {
if (property.isList() && ((main == null) || (main instanceof JsonArray)) &&((fork == null) || (fork instanceof JsonArray)) ) {
JsonArray arr1 = (JsonArray) main;
JsonArray arr2 = (JsonArray) fork;
for (int i = 0; i < Math.max(arrC(arr1), arrC(arr2)); i++) {
JsonElement m = arrI(arr1, i);
JsonElement f = arrI(arr2, i);
parseChildPrimitiveInstance(context, property, name, npath, m, f);
}
} else
parseChildPrimitiveInstance(context, property, name, npath, main, fork);
}
}
private JsonElement arrI(JsonArray arr, int i) {
return arr == null || i >= arr.size() || arr.get(i) instanceof JsonNull ? null : arr.get(i);
}
private int arrC(JsonArray arr) {
return arr == null ? 0 : arr.size();
}
private void parseChildPrimitiveInstance(Element context, Property property, String name, String npath,
JsonElement main, JsonElement fork) throws FHIRFormatError, DefinitionException {
if (main != null && !(main instanceof JsonPrimitive))
logError(line(main), col(main), npath, IssueType.INVALID, "This property must be an simple value, not a "+main.getClass().getName(), IssueSeverity.ERROR);
else if (fork != null && !(fork instanceof JsonObject))
logError(line(fork), col(fork), npath, IssueType.INVALID, "This property must be an object, not a "+fork.getClass().getName(), IssueSeverity.ERROR);
else {
Element n = new Element(name, property).markLocation(line(main != null ? main : fork), col(main != null ? main : fork));
context.getChildren().add(n);
if (main != null) {
JsonPrimitive p = (JsonPrimitive) main;
n.setValue(p.getAsString());
if (!n.getProperty().isChoice() && n.getType().equals("xhtml")) {
try {
n.setXhtml(new XhtmlParser().setValidatorMode(policy == ValidationPolicy.EVERYTHING).parse(n.getValue(), null).getDocumentElement());
} catch (Exception e) {
logError(line(main), col(main), npath, IssueType.INVALID, "Error parsing XHTML: "+e.getMessage(), IssueSeverity.ERROR);
}
}
if (policy == ValidationPolicy.EVERYTHING) {
// now we cross-check the primitive format against the stated type
if (Utilities.existsInList(n.getType(), "boolean")) {
if (!p.isBoolean())
logError(line(main), col(main), npath, IssueType.INVALID, "Error parsing JSON: the primitive value must be a boolean", IssueSeverity.ERROR);
} else if (Utilities.existsInList(n.getType(), "integer", "unsignedInt", "positiveInt", "decimal")) {
if (!p.isNumber())
logError(line(main), col(main), npath, IssueType.INVALID, "Error parsing JSON: the primitive value must be a number", IssueSeverity.ERROR);
} else if (!p.isString())
logError(line(main), col(main), npath, IssueType.INVALID, "Error parsing JSON: the primitive value must be a string", IssueSeverity.ERROR);
}
}
if (fork != null) {
JsonObject child = (JsonObject) fork;
checkObject(child, npath);
parseChildren(npath, child, n, false);
}
}
}
private void parseResource(String npath, JsonObject res, Element parent, Property elementProperty) throws DefinitionException, FHIRFormatError {
JsonElement rt = res.get("resourceType");
if (rt == null) {
logError(line(res), col(res), npath, IssueType.INVALID, "Unable to find resourceType property", IssueSeverity.FATAL);
} else {
String name = rt.getAsString();
StructureDefinition sd = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/"+name);
if (sd == null)
throw new FHIRFormatError("Contained resource does not appear to be a FHIR resource (unknown name '"+name+"')");
parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd), SpecialElement.fromProperty(parent.getProperty()), elementProperty);
parent.setType(name);
parseChildren(npath, res, parent, true);
}
}
private void reapComments(JsonObject object, Element context) {
if (object.has("fhir_comments")) {
JsonArray arr = object.getAsJsonArray("fhir_comments");
for (JsonElement e : arr) {
context.getComments().add(e.getAsString());
}
}
}
private int line(JsonElement e) {
if (map == null|| !map.containsKey(e))
return -1;
else
return map.get(e).getLine();
}
private int col(JsonElement e) {
if (map == null|| !map.containsKey(e))
return -1;
else
return map.get(e).getCol();
}
protected void prop(String name, String value, String link) throws IOException {
json.link(link);
if (name != null)
json.name(name);
json.value(value);
}
protected void open(String name, String link) throws IOException {
json.link(link);
if (name != null)
json.name(name);
json.beginObject();
}
protected void close() throws IOException {
json.endObject();
}
protected void openArray(String name, String link) throws IOException {
json.link(link);
if (name != null)
json.name(name);
json.beginArray();
}
protected void closeArray() throws IOException {
json.endArray();
}
@Override
public void compose(Element e, OutputStream stream, OutputStyle style, String identity) throws FHIRException, IOException {
OutputStreamWriter osw = new OutputStreamWriter(stream, "UTF-8");
if (style == OutputStyle.CANONICAL)
json = new JsonCreatorCanonical(osw);
else
json = new JsonCreatorGson(osw);
json.setIndent(style == OutputStyle.PRETTY ? " " : "");
json.beginObject();
prop("resourceType", e.getType(), null);
Set done = new HashSet();
for (Element child : e.getChildren()) {
compose(e.getName(), e, done, child);
}
json.endObject();
json.finish();
osw.flush();
}
public void compose(Element e, JsonCreator json) throws Exception {
this.json = json;
json.beginObject();
prop("resourceType", e.getType(), linkResolver == null ? null : linkResolver.resolveProperty(e.getProperty()));
Set done = new HashSet();
for (Element child : e.getChildren()) {
compose(e.getName(), e, done, child);
}
json.endObject();
json.finish();
}
private void compose(String path, Element e, Set done, Element child) throws IOException {
boolean isList = child.hasElementProperty() ? child.getElementProperty().isList() : child.getProperty().isList();
if (!isList) {// for specials, ignore the cardinality of the stated type
compose(path, child);
} else if (!done.contains(child.getName())) {
done.add(child.getName());
List list = e.getChildrenByName(child.getName());
composeList(path, list);
}
}
private void composeList(String path, List list) throws IOException {
// there will be at least one element
String name = list.get(0).getName();
boolean complex = true;
if (list.get(0).isPrimitive()) {
boolean prim = false;
complex = false;
for (Element item : list) {
if (item.hasValue())
prim = true;
if (item.hasChildren())
complex = true;
}
if (prim) {
openArray(name, linkResolver == null ? null : linkResolver.resolveProperty(list.get(0).getProperty()));
for (Element item : list) {
if (item.hasValue())
primitiveValue(null, item);
else
json.nullValue();
}
closeArray();
}
name = "_"+name;
}
if (complex) {
openArray(name, linkResolver == null ? null : linkResolver.resolveProperty(list.get(0).getProperty()));
for (Element item : list) {
if (item.hasChildren()) {
open(null,null);
if (item.getProperty().isResource()) {
prop("resourceType", item.getType(), linkResolver == null ? null : linkResolver.resolveType(item.getType()));
}
Set done = new HashSet();
for (Element child : item.getChildren()) {
compose(path+"."+name+"[]", item, done, child);
}
close();
} else
json.nullValue();
}
closeArray();
}
}
private void primitiveValue(String name, Element item) throws IOException {
if (name != null) {
if (linkResolver != null)
json.link(linkResolver.resolveProperty(item.getProperty()));
json.name(name);
}
String type = item.getType();
if (Utilities.existsInList(type, "boolean"))
json.value(item.getValue().trim().equals("true") ? new Boolean(true) : new Boolean(false));
else if (Utilities.existsInList(type, "integer", "unsignedInt", "positiveInt"))
json.value(new Integer(item.getValue()));
else if (Utilities.existsInList(type, "decimal"))
json.value(new BigDecimal(item.getValue()));
else
json.value(item.getValue());
}
private void compose(String path, Element element) throws IOException {
String name = element.getName();
if (element.isPrimitive() || isPrimitive(element.getType())) {
if (element.hasValue())
primitiveValue(name, element);
name = "_"+name;
}
if (element.hasChildren()) {
open(name, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
if (element.getProperty().isResource()) {
prop("resourceType", element.getType(), linkResolver == null ? null : linkResolver.resolveType(element.getType()));
}
Set done = new HashSet();
for (Element child : element.getChildren()) {
compose(path+"."+element.getName(), element, done, child);
}
close();
}
}
}
