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Builds the hapi fhir r4. Requires hapi-fhir-base and hapi-fhir-utilities be built first and be excluded from any other poms requiring it.
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package org.hl7.fhir.r4.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.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.r4.conformance.ProfileUtilities;
import org.hl7.fhir.r4.context.IWorkerContext;
import org.hl7.fhir.r4.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonCreator;
import org.hl7.fhir.r4.formats.JsonCreatorCanonical;
import org.hl7.fhir.r4.formats.JsonCreatorGson;
import org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r4.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.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;

  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, FHIRException {
    // if we're parsing at this point, then we're going to use the custom parser
    map = new IdentityHashMap();
    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 = JsonTrackingParser.parse(source, null); // (JsonObject) new
                                                               // com.google.gson.JsonParser().parse(source);
//			assert (map.containsKey(obj));
      return parse(obj);
    }
  }

  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, "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 FHIRException {
    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) {
      parseChildItem(path, object, context, 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,
              "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 context, Set processed,
      Property property, String name) throws FHIRException {
    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 {
      if (property.isList()) {
        logError(line(e), col(e), npath, IssueType.INVALID, "This property must be an Array, not " + describeType(e),
            IssueSeverity.ERROR);
      }
      parseChildComplexInstance(npath, object, context, 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, JsonObject object, Element context, 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));
      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 FHIRException {
    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 FHIRException {
    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 {
            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, s.getName() + " " + s.getValue(),
                    IssueSeverity.ERROR);
              }
            }
          } 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 FHIRException {
    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,
          ProfileUtilities.sdNs(name, context.getOverrideVersionNs()));
      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"))
      try {
        json.value(new BigDecimal(item.getValue()));
      } catch (Exception e) {
        throw new NumberFormatException("error writing number '" + item.getValue() + "' to JSON");
      }
    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();
    }
  }

}