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package org.hl7.fhir.r4b.elementmodel;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r4b.conformance.ProfileUtilities;
import org.hl7.fhir.r4b.context.IWorkerContext;
import org.hl7.fhir.r4b.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r4b.fhirpath.FHIRPathEngine;
import org.hl7.fhir.r4b.formats.IParser.OutputStyle;
import org.hl7.fhir.r4b.formats.JsonCreator;
import org.hl7.fhir.r4b.formats.JsonCreatorCanonical;
import org.hl7.fhir.r4b.formats.JsonCreatorGson;
import org.hl7.fhir.r4b.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r4b.model.StructureDefinition;
import org.hl7.fhir.utilities.StringPair;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.json.JsonTrackingParser.LocationData;
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;
private boolean allowComments;
private ProfileUtilities profileUtilities;
public JsonParser(IWorkerContext context, ProfileUtilities utilities) {
super(context);
this.profileUtilities = utilities;
}
public JsonParser(IWorkerContext context) {
super(context);
this.profileUtilities = new ProfileUtilities(this.context, null, null, new FHIRPathEngine(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, this.profileUtilities));
result.setPath(type);
checkObject(obj, path);
result.setType(type);
parseChildren(path, obj, result, true);
result.numberChildren();
return result;
}
@Override
public List parse(InputStream stream) throws IOException, FHIRException {
// if we're parsing at this point, then we're going to use the custom parser
List res = new ArrayList<>();
map = new IdentityHashMap();
String source = TextFile.streamToString(stream);
if (policy == ValidationPolicy.EVERYTHING) {
JsonObject obj = null;
try {
obj = JsonTrackingParser.parse(source, map, false, allowComments);
} catch (Exception e) {
logError(-1, -1, context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID,
context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
return null;
}
assert (map.containsKey(obj));
Element e = parse(obj);
if (e != null) {
res.add(new NamedElement(null, e));
}
} else {
JsonObject obj = JsonTrackingParser.parse(source, null); // (JsonObject) new
// com.google.gson.JsonParser().parse(source);
// assert (map.containsKey(obj));
Element e = parse(obj);
if (e != null) {
res.add(new NamedElement(null, e));
}
}
return res;
}
public Element parse(JsonObject object, Map map) throws FHIRException {
this.map = map;
return parse(object);
}
public Element parse(JsonObject object) throws FHIRException {
JsonElement rt = object.get("resourceType");
if (rt == null) {
logError(line(object), col(object), "$", IssueType.INVALID,
context.formatMessage(I18nConstants.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, this.profileUtilities));
checkObject(object, path);
result.markLocation(line(object), col(object));
result.setType(name);
result.setPath(result.fhirType());
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,
context.formatMessage(I18nConstants.OBJECT_MUST_HAVE_SOME_CONTENT), IssueSeverity.ERROR);
}
}
private void parseChildren(String path, JsonObject object, Element element, boolean hasResourceType)
throws FHIRException {
reapComments(object, element);
List properties = element.getProperty().getChildProperties(element.getName(), null);
Set processed = new HashSet();
if (hasResourceType)
processed.add("resourceType");
// 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) {
parseChildItem(path, object, element, processed, property);
}
// 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,
context.formatMessage(I18nConstants.UNRECOGNISED_PROPERTY_, e.getKey()), IssueSeverity.ERROR);
}
}
}
}
public void parseChildItem(String path, JsonObject object, Element context, Set processed,
Property property) {
if (property.isChoice() || property.getDefinition().getPath().endsWith("data[x]")) {
for (TypeRefComponent type : property.getDefinition().getType()) {
String eName = property.getName().substring(0, property.getName().length() - 3)
+ Utilities.capitalize(type.getWorkingCode());
if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) {
parseChildComplex(path, object, context, processed, property, eName);
break;
} else if (isPrimitive(type.getWorkingCode()) && (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());
}
}
private void parseChildComplex(String path, JsonObject object, Element element, Set processed,
Property property, String name) throws FHIRException {
processed.add(name);
String npath = path + "." + property.getName();
String fpath = element.getPath() + "." + property.getName();
JsonElement e = object.get(name);
if (property.isList() && (e instanceof JsonArray)) {
JsonArray arr = (JsonArray) e;
if (arr.size() == 0) {
logError(line(e), col(e), npath, IssueType.INVALID, context.formatMessage(I18nConstants.ARRAY_CANNOT_BE_EMPTY),
IssueSeverity.ERROR);
}
int c = 0;
for (JsonElement am : arr) {
parseChildComplexInstance(npath + "[" + c + "]", fpath + "[" + c + "]", object, element, property, name, am);
c++;
}
} else {
if (property.isList()) {
logError(line(e), col(e), npath, IssueType.INVALID,
context.formatMessage(I18nConstants.THIS_PROPERTY_MUST_BE_AN_ARRAY_NOT_, describeType(e), name, path),
IssueSeverity.ERROR);
}
parseChildComplexInstance(npath, fpath, object, element, property, name, e);
}
}
private String describeType(JsonElement e) {
if (e.isJsonArray())
return "an Array";
if (e.isJsonObject())
return "an Object";
if (e.isJsonPrimitive())
return "a primitive property";
if (e.isJsonNull())
return "a Null";
return null;
}
private void parseChildComplexInstance(String npath, String fpath, JsonObject object, Element element,
Property property, String name, JsonElement e) throws FHIRException {
if (e instanceof JsonObject) {
JsonObject child = (JsonObject) e;
Element n = new Element(name, property).markLocation(line(child), col(child));
n.setPath(fpath);
checkObject(child, npath);
element.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,
context.formatMessage(I18nConstants.THIS_PROPERTY_MUST_BE__NOT_,
(property.isList() ? "an Array" : "an Object"), describe(e), name, npath),
IssueSeverity.ERROR);
}
private String describe(JsonElement e) {
if (e instanceof JsonArray) {
return "an array";
}
if (e instanceof JsonObject) {
return "an object";
}
if (e instanceof JsonNull) {
return "null";
}
return "a primitive property";
}
private void parseChildPrimitive(JsonObject object, Element element, Set processed, Property property,
String path, String name) throws FHIRException {
String npath = path + "." + property.getName();
String fpath = element.getPath() + "." + 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()) {
boolean ok = true;
if (!(main == null || main instanceof JsonArray)) {
logError(line(main), col(main), npath, IssueType.INVALID,
context.formatMessage(I18nConstants.THIS_PROPERTY_MUST_BE_AN_ARRAY_NOT_, describe(main), name, path),
IssueSeverity.ERROR);
ok = false;
}
if (!(fork == null || fork instanceof JsonArray)) {
logError(line(fork), col(fork), npath, IssueType.INVALID,
context.formatMessage(I18nConstants.THIS_BASE_PROPERTY_MUST_BE_AN_ARRAY_NOT_, describe(main), name, path),
IssueSeverity.ERROR);
ok = false;
}
if (ok) {
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(element, property, name, npath, fpath, m, f);
}
}
} else {
parseChildPrimitiveInstance(element, property, name, npath, fpath, 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 element, Property property, String name, String npath, String fpath,
JsonElement main, JsonElement fork) throws FHIRException {
if (main != null && !(main instanceof JsonPrimitive))
logError(line(main), col(main), npath, IssueType.INVALID,
context.formatMessage(I18nConstants.THIS_PROPERTY_MUST_BE_AN_SIMPLE_VALUE_NOT_, describe(main), name, npath),
IssueSeverity.ERROR);
else if (fork != null && !(fork instanceof JsonObject))
logError(line(fork), col(fork), npath, IssueType.INVALID,
context.formatMessage(I18nConstants.THIS_PROPERTY_MUST_BE_AN_OBJECT_NOT_, describe(fork), name, npath),
IssueSeverity.ERROR);
else {
Element n = new Element(name, property).markLocation(line(main != null ? main : fork),
col(main != null ? main : fork));
n.setPath(fpath);
element.getChildren().add(n);
if (main != null) {
JsonPrimitive p = (JsonPrimitive) main;
if (p.isNumber() && p.getAsNumber() instanceof JsonTrackingParser.PresentedBigDecimal) {
String rawValue = ((JsonTrackingParser.PresentedBigDecimal) p.getAsNumber()).getPresentation();
n.setValue(rawValue);
} else {
n.setValue(p.getAsString());
}
if (!n.getProperty().isChoice() && n.getType().equals("xhtml")) {
try {
XhtmlParser xp = new XhtmlParser();
n.setXhtml(xp.parse(n.getValue(), null).getDocumentElement());
if (policy == ValidationPolicy.EVERYTHING) {
for (StringPair s : xp.getValidationIssues()) {
logError(line(main), col(main), npath, IssueType.INVALID,
context.formatMessage(s.getName(), s.getValue()), IssueSeverity.ERROR);
}
}
} catch (Exception e) {
logError(line(main), col(main), npath, IssueType.INVALID,
context.formatMessage(I18nConstants.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,
context.formatMessage(I18nConstants.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,
context.formatMessage(I18nConstants.ERROR_PARSING_JSON_THE_PRIMITIVE_VALUE_MUST_BE_A_NUMBER),
IssueSeverity.ERROR);
} else if (!p.isString())
logError(line(main), col(main), npath, IssueType.INVALID,
context.formatMessage(I18nConstants.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 FHIRException {
JsonElement rt = res.get("resourceType");
if (rt == null) {
logError(line(res), col(res), npath, IssueType.INVALID,
context.formatMessage(I18nConstants.UNABLE_TO_FIND_RESOURCETYPE_PROPERTY), IssueSeverity.FATAL);
} else {
String name = rt.getAsString();
StructureDefinition sd = context.fetchResource(StructureDefinition.class,
ProfileUtilities.sdNs(name, context.getOverrideVersionNs()));
if (sd == null) {
logError(line(res), col(res), npath, IssueType.INVALID, context
.formatMessage(I18nConstants.CONTAINED_RESOURCE_DOES_NOT_APPEAR_TO_BE_A_FHIR_RESOURCE_UNKNOWN_NAME_, name),
IssueSeverity.FATAL);
} else {
parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd, this.profileUtilities),
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"))
try {
json.value(new BigDecimal(item.getValue()));
} catch (Exception e) {
throw new NumberFormatException(
context.formatMessage(I18nConstants.ERROR_WRITING_NUMBER__TO_JSON, 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.getType().equals("xhtml"))
json.anchor("end-xhtml");
}
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();
}
}
public boolean isAllowComments() {
return allowComments;
}
public JsonParser setAllowComments(boolean allowComments) {
this.allowComments = allowComments;
return this;
}
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