/**
    * The contents of this file are subject to the Mozilla Public License Version 1.1
    * (the "License"); you may not use this file except in compliance with the License.
    * You may obtain a copy of the License at http://www.mozilla.org/MPL/
    * Software distributed under the License is distributed on an "AS IS" basis,
    * WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for the
    * specific language governing rights and limitations under the License.
    *
    * The Original Code is "PipeParser.java".  Description:
   * "An implementation of Parser that supports traditionally encoded (i.e"
   *
   * The Initial Developer of the Original Code is University Health Network. Copyright (C)
   * 2001.  All Rights Reserved.
   *
   * Contributor(s): Kenneth Beaton.
   *
   * Alternatively, the contents of this file may be used under the terms of the
   * GNU General Public License (the  "GPL"), in which case the provisions of the GPL are
   * applicable instead of those above.  If you wish to allow use of your version of this
   * file only under the terms of the GPL and not to allow others to use your version
   * of this file under the MPL, indicate your decision by deleting  the provisions above
   * and replace  them with the notice and other provisions required by the GPL License.
   * If you do not delete the provisions above, a recipient may use your version of
   * this file under either the MPL or the GPL.
   *
   */
  
  package ca.uhn.hl7v2.parser;
  
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  import java.util.Set;
  import java.util.StringTokenizer;
  
  import ca.uhn.hl7v2.validation.ValidationContext;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  import ca.uhn.hl7v2.DefaultHapiContext;
  import ca.uhn.hl7v2.ErrorCode;
  import ca.uhn.hl7v2.HL7Exception;
  import ca.uhn.hl7v2.HapiContext;
  import ca.uhn.hl7v2.Version;
  import ca.uhn.hl7v2.model.AbstractSuperMessage;
  import ca.uhn.hl7v2.model.DoNotCacheStructure;
  import ca.uhn.hl7v2.model.Group;
  import ca.uhn.hl7v2.model.Message;
  import ca.uhn.hl7v2.model.Primitive;
  import ca.uhn.hl7v2.model.Segment;
  import ca.uhn.hl7v2.model.Structure;
  import ca.uhn.hl7v2.model.SuperStructure;
  import ca.uhn.hl7v2.model.Type;
  import ca.uhn.hl7v2.model.Varies;
  import ca.uhn.hl7v2.util.ReflectionUtil;
  import ca.uhn.hl7v2.util.Terser;
  import ca.uhn.hl7v2.validation.impl.NoValidation;
  import ca.uhn.hl7v2.validation.impl.ValidationContextFactory;
  
  /**
   * An implementation of Parser that supports traditionally encoded (ie delimited
   * with characters like |, ^, and ~) HL7 messages. Unexpected segments and
   * fields are parsed into generic elements that are added to the message.
   * 
   * @see ParserConfiguration for configuration options which may affect parser encoding and decoding behaviour
   * @author Bryan Tripp (bryan_tripp@sourceforge.net)
   */
  public class PipeParser extends Parser {
  
  	private static final Logger log = LoggerFactory.getLogger(PipeParser.class);
  
  	/**
  	 * The HL7 ER7 segment delimiter (see section 2.8 of spec)
  	 */
  	final static String SEGMENT_DELIMITER = "\r";
  
  	private final HashMap<Class<? extends Message>, HashMap<String, StructureDefinition>> myStructureDefinitions = new HashMap<>();
  
  	/**
  	 * System property key. If value is "true", legacy mode will default to true
  	 * 
  	 * @see #isLegacyMode()
  	 * @deprecated This will be removed in HAPI 3.0
  	 */
  	public static final String DEFAULT_LEGACY_MODE_PROPERTY = "ca.uhn.hl7v2.parser.PipeParser.default_legacy_mode";
  
  	private Boolean myLegacyMode = null;
  
  	public PipeParser() {
  		super();
  	}
  
  	/**
  	 * @param context
  	 *            the context containing all configuration items to be used
  	 */
  	public PipeParser(HapiContext context) {
 		super(context);
 	}
 
 	/**
 	 * Creates a new PipeParser
 	 * 
 	 * @param theFactory
 	 *            custom factory to use for model class lookup
 	 */
 	public PipeParser(ModelClassFactory theFactory) {
 		super(theFactory);
 	}
 
     @Override
     public void setValidationContext(ValidationContext context) {
         super.setValidationContext(context);
     }
 
     /**
 	 * Returns a String representing the encoding of the given message, if the
 	 * encoding is recognized. For example if the given message appears to be
 	 * encoded using HL7 2.x XML rules then "XML" would be returned. If the
 	 * encoding is not recognized then null is returned. That this method
 	 * returns a specific encoding does not guarantee that the message is
 	 * correctly encoded (e.g. well formed XML) - just that it is not encoded
 	 * using any other encoding than the one returned.
 	 */
 	public String getEncoding(String message) {
 		return EncodingDetector.isEr7Encoded(message) ? getDefaultEncoding() : null;
 	}
 
 	/**
 	 * @return the preferred encoding of this Parser
 	 */
 	public String getDefaultEncoding() {
 		return "VB";
 	}
 
 	/**
 	 * @deprecated this method should not be public
 	 * @param message HL7 message
 	 * @return message structure
 	 * @throws HL7Exception
 	 */
 	public String getMessageStructure(String message) throws HL7Exception {
 		return getStructure(message).messageStructure;
 	}
 
 	/**
 	 * @return the message structure from MSH-9-3
 	 */
 	private MessageStructure getStructure(String message) throws HL7Exception {
 		EncodingCharacters ec = getEncodingChars(message);
 		String messageStructure;
 		boolean explicityDefined = true;
 		String wholeFieldNine;
 		try {
 			String[] fields = split(message.substring(0, Math.max(message.indexOf(SEGMENT_DELIMITER), message.length())), String.valueOf(ec.getFieldSeparator()));
 			wholeFieldNine = fields[8];
 
 			// message structure is component 3 but we'll accept a composite of
 			// 1 and 2 if there is no component 3 ...
 			// if component 1 is ACK, then the structure is ACK regardless of
 			// component 2
 			String[] comps = split(wholeFieldNine, String.valueOf(ec.getComponentSeparator()));
 			if (comps.length >= 3) {
 				messageStructure = comps[2];
 			} else if (comps.length > 0 && comps[0] != null && comps[0].equals("ACK")) {
 				messageStructure = "ACK";
 			} else if (comps.length == 2) {
 				explicityDefined = false;
 				messageStructure = comps[0] + "_" + comps[1];
 			}
 			/*
 			 * else if (comps.length == 1 && comps[0] != null &&
 			 * comps[0].equals("ACK")) { messageStructure = "ACK"; //it's common
 			 * for people to only populate component 1 in an ACK msg }
 			 */
 			else {
 				String buf = "Can't determine message structure from MSH-9: " + wholeFieldNine +
 						" HINT: there are only " +
 						comps.length +
 						" of 3 components present";
 				throw new HL7Exception(buf, ErrorCode.UNSUPPORTED_MESSAGE_TYPE);
 			}
 		} catch (IndexOutOfBoundsException e) {
 			throw new HL7Exception("Can't find message structure (MSH-9-3): " + e.getMessage(), ErrorCode.UNSUPPORTED_MESSAGE_TYPE);
 		}
 
 		return new MessageStructure(messageStructure, explicityDefined);
 	}
 
 	/**
 	 * Returns object that contains the field separator and encoding characters
 	 * for this message.
 	 *
 	 * There's an additional character starting with v2.7 (truncation), but we will
 	 * accept it in messages of any version.
 	 * 
 	 * @throws HL7Exception
 	 */
 	private static EncodingCharacters getEncodingChars(String message) throws HL7Exception {
 		if (message.length() < 9) {
 			throw new HL7Exception("Invalid message content: \"" + message + "\"");
 		}
 		return new EncodingCharacters(message.charAt(3), message.substring(4, 9));
 	}
 
 	/**
 	 * Parses a message string and returns the corresponding Message object.
 	 * Unexpected segments added at the end of their group.
 	 * 
 	 * @throws HL7Exception
 	 *             if the message is not correctly formatted.
 	 * @throws EncodingNotSupportedException
 	 *             if the message encoded is not supported by this parser.
 	 */
 	protected Message doParse(String message, String version) throws HL7Exception {
 
 		// try to instantiate a message object of the right class
 		MessageStructure structure = getStructure(message);
 		Message m = instantiateMessage(structure.messageStructure, version, structure.explicitlyDefined);
 		m.setParser(this);
 		parse(m, message);
 		return m;
 	}
 
 	/**
 	 * {@inheritDoc}
 	 */
 	protected Message doParseForSpecificPackage(String message, String version, String packageName) throws HL7Exception {
 
 		// try to instantiate a message object of the right class
 		MessageStructure structure = getStructure(message);
 		Message m = instantiateMessageInASpecificPackage(structure.messageStructure, version, structure.explicitlyDefined, packageName);
 
 		parse(m, message);
 
 		return m;
 	}
 
 	/**
 	 * Generates (or returns the cached value of) the message
 	 */
 	private IStructureDefinition getStructureDefinition(Message theMessage) throws HL7Exception {
 
 		Class<? extends Message> clazz = theMessage.getClass();
 		HashMap<String, StructureDefinition> definitions = myStructureDefinitions.get(clazz);
 
 		StructureDefinition retVal;
 		if (definitions != null) {
 			retVal = definitions.get(theMessage.getName());
 			if (retVal != null) {
 				return retVal;
 			}
 		}
 
 		if (theMessage instanceof SuperStructure) {
 			Set<String> appliesTo = ((SuperStructure) theMessage).getStructuresWhichChildAppliesTo("MSH");
 			if (!appliesTo.contains(theMessage.getName())) {
 				throw new HL7Exception("Superstructure " + theMessage.getClass().getSimpleName() + " does not apply to message " + theMessage.getName() + ", can not parse.");
 			}
 		}
 		
 		if (clazz.isAnnotationPresent(DoNotCacheStructure.class)) {
 			Holder<StructureDefinition> previousLeaf = new Holder<>();
 			retVal = createStructureDefinition(theMessage, previousLeaf, theMessage.getName());
 		} else {
 			Message message = ReflectionUtil.instantiateMessage(clazz, getFactory());
 			Holder<StructureDefinition> previousLeaf = new Holder<>();
 			retVal = createStructureDefinition(message, previousLeaf, theMessage.getName());
 
 			if (!myStructureDefinitions.containsKey(clazz)) {
 				myStructureDefinitions.put(clazz, new HashMap<>());
 			}
 			myStructureDefinitions.get(clazz).put(theMessage.getName(), retVal);
 		}
 
 		return retVal;
 	}
 
 	private StructureDefinition createStructureDefinition(Structure theStructure, Holder<StructureDefinition> thePreviousLeaf, String theStructureName) throws HL7Exception {
 
 		StructureDefinition retVal = new StructureDefinition();
 		retVal.setName(theStructure.getName());
 
 		if (theStructure instanceof Group) {
 			retVal.setSegment(false);
 			Group group = (Group) theStructure;
 			int index = 0;
 			List<String> childNames = Arrays.asList(group.getNames());
 			
 			/*
 			 * For SuperStructures, which can hold more than one type of structure,
 			 * we only actually bring in the child names that are actually a part
 			 * of the structure we are trying to parse
 			 */
 			if (theStructure instanceof SuperStructure) {
 				String struct = theStructureName;
 				Map<String, String> evtMap = new DefaultModelClassFactory().getEventMapForVersion(Version.versionOf(theStructure.getMessage().getVersion()));
 				if (evtMap.containsKey(struct)) {
 					struct = evtMap.get(struct);
 				}
 				childNames = ((SuperStructure) theStructure).getChildNamesForStructure(struct);
 			}
 			
 			for (String nextName : childNames) {
 				Structure nextChild = group.get(nextName);
 				StructureDefinition structureDefinition = createStructureDefinition(nextChild, thePreviousLeaf, theStructureName);
 				structureDefinition.setNameAsItAppearsInParent(nextName);
 				structureDefinition.setRepeating(group.isRepeating(nextName));
 				structureDefinition.setRequired(group.isRequired(nextName));
 				structureDefinition.setChoiceElement(group.isChoiceElement(nextName));
 				structureDefinition.setPosition(index++);
 				structureDefinition.setParent(retVal);
 				retVal.addChild(structureDefinition);
 			}
 		} else {
 			if (thePreviousLeaf.getObject() != null) {
 				thePreviousLeaf.getObject().setNextLeaf(retVal);
 			}
 			thePreviousLeaf.setObject(retVal);
 			retVal.setSegment(true);
 		}
 
 		return retVal;
 	}
 
 	/**
 	 * Parses a segment string and populates the given Segment object.
 	 * Unexpected fields are added as Varies' at the end of the segment.
      *
 	 * @param destination segment to parse the segment string into
      * @param segment encoded segment
      * @param encodingChars encoding characters to be used
 	 * @throws HL7Exception
 	 *             if the given string does not contain the given segment or if
 	 *             the string is not encoded properly
 	 */
 	public void parse(Segment destination, String segment, EncodingCharacters encodingChars) throws HL7Exception {
 		parse(destination, segment, encodingChars, 0);
 	}
 
 	/**
 	 * Parses a segment string and populates the given Segment object.
 	 * Unexpected fields are added as Varies' at the end of the segment.
 	 *
      * @param destination segment to parse the segment string into
      * @param segment encoded segment
      * @param encodingChars encoding characters to be used
 	 * @param theRepetition the repetition number of this segment within its group
 	 * @throws HL7Exception
 	 *             if the given string does not contain the given segment or if
 	 *             the string is not encoded properly
 	 */
 	public void parse(Segment destination, String segment, EncodingCharacters encodingChars, int theRepetition) throws HL7Exception {
 		int fieldOffset = 0;
 		if (isDelimDefSegment(destination.getName())) {
 			fieldOffset = 1;
 			// set field 1 to fourth character of string
 			Terser.set(destination, 1, 0, 1, 1, String.valueOf(encodingChars.getFieldSeparator()));
 		}
 
 		String[] fields = split(segment, String.valueOf(encodingChars.getFieldSeparator()));
 		// destination.setName(fields[0]);
 		for (int i = 1; i < fields.length; i++) {
 			String[] reps = split(fields[i], String.valueOf(encodingChars.getRepetitionSeparator()));
 
 			// MSH-2 will get split incorrectly so we have to fudge it ...
 			boolean isMSH2 = isDelimDefSegment(destination.getName()) && i + fieldOffset == 2;
 			if (isMSH2) {
 				reps = new String[1];
 				reps[0] = fields[i];
 			}
 
 			for (int j = 0; j < reps.length; j++) {
 				try {
 					log.trace("Parsing field {} repetition {}", i + fieldOffset, j);
 					Type field = destination.getField(i + fieldOffset, j);
 					if (isMSH2) {
 						Terser.getPrimitive(field, 1, 1).setValue(reps[j]);
 					} else {
 						parse(field, reps[j], encodingChars);
 					}
 				} catch (HL7Exception e) {
 					// set the field location and throw again ...
 					e.setFieldPosition(i);
 					if (theRepetition > 1) {
 						e.setSegmentRepetition(theRepetition);
 					}
 					e.setSegmentName(destination.getName());
 					throw e;
 				}
 			}
 		}
 
 		// set data type of OBX-5
 		if (destination.getClass().getName().contains("OBX")) {
 			FixFieldDataType.fixOBX5(destination, getFactory(), getHapiContext().getParserConfiguration());
 		}
         // set data type of MFE-4
         if (destination.getClass().getName().contains("MFE") &&
                 Version.versionOf(destination.getMessage().getVersion()).isGreaterThan(Version.V23)) {
             FixFieldDataType.fixMFE4(destination, getFactory(), getHapiContext().getParserConfiguration());
         }
 
 	}
 
 	/**
 	 * @return true if the segment is MSH, FHS, or BHS. These need special
 	 *         treatment because they define delimiters.
 	 * @param theSegmentName
 	 *            segment name
 	 */
 	private static boolean isDelimDefSegment(String theSegmentName) {
 		boolean is = false;
 		if (theSegmentName.equals("MSH") || theSegmentName.equals("FHS") || theSegmentName.equals("BHS")) {
 			is = true;
 		}
 		return is;
 	}
 
 	/**
 	 * Fills a field with values from an unparsed string representing the field.
 	 * 
 	 * @param destinationField
 	 *            the field Type
 	 * @param data
 	 *            the field string (including all components and subcomponents;
 	 *            not including field delimiters)
 	 * @param encodingCharacters
 	 *            the encoding characters used in the message
 	 */
 	@Override
 	public void parse(Type destinationField, String data, EncodingCharacters encodingCharacters) throws HL7Exception {
 		String[] components = split(data, String.valueOf(encodingCharacters.getComponentSeparator()));
 		for (int i = 0; i < components.length; i++) {
 			String[] subcomponents = split(components[i], String.valueOf(encodingCharacters.getSubcomponentSeparator()));
 			for (int j = 0; j < subcomponents.length; j++) {
 				String val = subcomponents[j];
 				if (val != null) {
 					val = getParserConfiguration().getEscaping().unescape(val, encodingCharacters);
 				}
 				Terser.getPrimitive(destinationField, i + 1, j + 1).setValue(val);
 			}
 		}
 	}
 
 	/**
 	 * Splits the given composite string into an array of components using the
 	 * given delimiter.
      *
      * @param composite encoded composite string
      * @param delim delimiter to split upon
      * @return split string
 	 */
 	public static String[] split(String composite, String delim) {
 		ArrayList<String> components = new ArrayList<>();
 
 		// defend against evil nulls
 		if (composite == null)
 			composite = "";
 		if (delim == null)
 			delim = "";
 
 		StringTokenizer tok = new StringTokenizer(composite, delim, true);
 		boolean previousTokenWasDelim = true;
 		while (tok.hasMoreTokens()) {
 			String thisTok = tok.nextToken();
 			if (thisTok.equals(delim)) {
 				if (previousTokenWasDelim)
 					components.add(null);
 				previousTokenWasDelim = true;
 			} else {
 				components.add(thisTok);
 				previousTokenWasDelim = false;
 			}
 		}
 
 		String[] ret = new String[components.size()];
 		for (int i = 0; i < components.size(); i++) {
 			ret[i] = components.get(i);
 		}
 
 		return ret;
 	}
 
 	/**
 	 * {@inheritDoc }
 	 */
 	@Override
 	public String doEncode(Segment structure, EncodingCharacters encodingCharacters) {
 		return encode(structure, encodingCharacters, getParserConfiguration(), null);
 	}
 
 	/**
 	 * {@inheritDoc }
 	 */
 	@Override
 	public String doEncode(Type type, EncodingCharacters encodingCharacters) {
 		return encode(type, encodingCharacters, getParserConfiguration(), null);
 	}
 
 	/**
 	 * Encodes the given Type, using the given encoding characters. It is
 	 * assumed that the Type represents a complete field rather than a
 	 * component.
      *
      * @param source type to be encoded
      * @param encodingChars encoding characters to be used
      * @return encoded type
 	 */
 	public static String encode(Type source, EncodingCharacters encodingChars) {
 		return encode(source, encodingChars, source.getMessage().getParser().getParserConfiguration(), null);
 	}
 
 	private static String encode(Type source, EncodingCharacters encodingChars, ParserConfiguration parserConfig, String currentTerserPath) {
 		if (source instanceof Varies) {
 			Varies varies = (Varies) source;
 			if (varies.getData() != null) {
 				source = varies.getData();
 			}
 		}
 
 		StringBuilder field = new StringBuilder();
 		for (int i = 1; i <= Terser.numComponents(source); i++) {
 			StringBuilder comp = new StringBuilder();
 			for (int j = 1; j <= Terser.numSubComponents(source, i); j++) {
 				Primitive p = Terser.getPrimitive(source, i, j);
 				comp.append(encodePrimitive(p, parserConfig.getEscaping(), encodingChars));
 				comp.append(encodingChars.getSubcomponentSeparator());
 			}
 			field.append(stripExtraDelimiters(comp.toString(), encodingChars.getSubcomponentSeparator()));
 			field.append(encodingChars.getComponentSeparator());
 		}
 
 		int forceUpToFieldNum = 0;
 		if (parserConfig != null && currentTerserPath != null) {
 			for (String nextPath : parserConfig.getForcedEncode()) {
 				if (nextPath.startsWith(currentTerserPath + "-") && nextPath.length() > currentTerserPath.length()) {
 					int endOfFieldDef = nextPath.indexOf('-', currentTerserPath.length());
 					if (endOfFieldDef == -1) {
 						forceUpToFieldNum = 0;
 						break;
 					}
 					String fieldNumString = nextPath.substring(endOfFieldDef + 1);
 					if (fieldNumString.length() > 0) {
 						forceUpToFieldNum = Math.max(forceUpToFieldNum, Integer.parseInt(fieldNumString));
 					}
 				}
 			}
 		}
 
 		char componentSeparator = encodingChars.getComponentSeparator();
 		String retVal = stripExtraDelimiters(field.toString(), componentSeparator);
 
 		while (forceUpToFieldNum > 0 && (countInstancesOf(retVal, componentSeparator) + 1) < forceUpToFieldNum) {
 			retVal = retVal + componentSeparator;
 		}
 
 		return retVal;
 	}
 
 	private static String encodePrimitive(Primitive p, Escaping escaping, EncodingCharacters encodingChars) {
 		String val = (p).getValue();
 		if (val == null) {
 			val = "";
 		} else {
 			val = escaping.escape(val, encodingChars);
 		}
 		return val;
 	}
 
 	/**
 	 * Removes unecessary delimiters from the end of a field or segment. This
 	 * seems to be more convenient than checking to see if they are needed while
 	 * we are building the encoded string.
 	 */
 	private static String stripExtraDelimiters(String in, char delim) {
 		char[] chars = in.toCharArray();
 
 		// search from back end for first occurance of non-delimiter ...
 		int c = chars.length - 1;
 		boolean found = false;
 		while (c >= 0 && !found) {
 			if (chars[c--] != delim)
 				found = true;
 		}
 
 		String ret = "";
 		if (found)
 			ret = String.valueOf(chars, 0, c + 2);
 		return ret;
 	}
 
 	/**
 	 * Formats a Message object into an HL7 message string using the given
 	 * encoding.
 	 * 
 	 * @throws HL7Exception
 	 *             if the data fields in the message do not permit encoding
 	 *             (e.g. required fields are null)
 	 * @throws EncodingNotSupportedException
 	 *             if the requested encoding is not supported by this parser.
 	 */
 	protected String doEncode(Message source, String encoding) throws HL7Exception {
 		if (!this.supportsEncoding(encoding))
 			throw new EncodingNotSupportedException("This parser does not support the " + encoding + " encoding");
 
 		return encode(source);
 	}
 
 	/**
 	 * Formats a Message object into an HL7 message string using this parser's
 	 * default encoding ("VB").
 	 * 
 	 * @throws HL7Exception
 	 *             if the data fields in the message do not permit encoding
 	 *             (e.g. required fields are null)
 	 */
 	protected String doEncode(Message source) throws HL7Exception {
 		// get encoding characters ...
 		Segment msh = (Segment) source.get("MSH");
 		String fieldSepString = Terser.get(msh, 1, 0, 1, 1);
 
 		if (fieldSepString == null)
 			throw new HL7Exception("Can't encode message: MSH-1 (field separator) is missing");
 
 		char fieldSep = '|';
 		if (fieldSepString.length() > 0) fieldSep = fieldSepString.charAt(0);
 
 		EncodingCharacters en = getValidEncodingCharacters(fieldSep, msh);
 
 		// pass down to group encoding method which will operate recursively on
 		// children ...
 		return encode(source, en, getParserConfiguration(), "");
 	}
 
 	private EncodingCharacters getValidEncodingCharacters(char fieldSep, Segment msh) throws HL7Exception {
 		String encCharString = Terser.get(msh, 2, 0, 1, 1);
 
 		if (encCharString == null) {
 			throw new HL7Exception("Can't encode message: MSH-2 (encoding characters) is missing");
 		}
 
 		if (Version.V27.isGreaterThan(Version.versionOf(msh.getMessage().getVersion())) && encCharString.length() != 4) {
 			throw new HL7Exception("Encoding characters (MSH-2) value '" + encCharString + "' invalid -- must be 4 characters", ErrorCode.DATA_TYPE_ERROR);
 		} else if (encCharString.length() != 4 && encCharString.length() != 5) {
 			throw new HL7Exception("Encoding characters (MSH-2) value '" + encCharString + "' invalid -- must be 4 or 5 characters", ErrorCode.DATA_TYPE_ERROR);
 		}
 
 		return new EncodingCharacters(fieldSep, encCharString);
 	}
 
 	/**
 	 * Returns given group serialized as a pipe-encoded string - this method is
 	 * called by encode(Message source, String encoding).
      *
      * @param source group to be encoded
      * @param encodingChars encoding characters to be used
      * @throws HL7Exception if an error occurred while encoding
      * @return encoded group
 	 */
 	public static String encode(Group source, EncodingCharacters encodingChars) throws HL7Exception {
 		return encode(source, encodingChars, source.getMessage().getParser().getParserConfiguration(), "");
 	}
 
 	/**
 	 * Returns given group serialized as a pipe-encoded string - this method is
 	 * called by encode(Message source, String encoding).
 	 */
 	private static String encode(Group source, EncodingCharacters encodingChars, ParserConfiguration parserConfiguration, String currentTerserPath) throws HL7Exception {
 		StringBuilder result = new StringBuilder();
 
 		String[] names = source.getNames();
 
 		String firstMandatorySegmentName = null;
 		boolean haveEncounteredMandatorySegment = false;
 		boolean haveEncounteredContent = false;
 		boolean haveHadMandatorySegment = false;
 		boolean haveHadSegmentBeforeMandatorySegment = false;
 
 		for (String nextName : names) {
 
 			// source.get(nextName, 0);
 			Structure[] reps = source.getAll(nextName);
 			boolean nextNameIsRequired = source.isRequired(nextName);
 
 			boolean havePreviouslyEncounteredMandatorySegment = haveEncounteredMandatorySegment;
 			haveEncounteredMandatorySegment |= nextNameIsRequired;
 			if (nextNameIsRequired && !haveHadMandatorySegment) {
 				if (!source.isGroup(nextName)) {
 					firstMandatorySegmentName = nextName;
 				}
 			}
 
 			String nextTerserPath = currentTerserPath.length() > 0 ? currentTerserPath + "/" + nextName : nextName;
 
 			// Add all reps of the next segment/group
 			for (Structure rep : reps) {
 
 				if (rep instanceof Group) {
 
 					String encodedGroup = encode((Group) rep, encodingChars, parserConfiguration, nextTerserPath);
 					result.append(encodedGroup);
 
 					if (encodedGroup.length() > 0) {
 						if (!haveHadMandatorySegment && !haveEncounteredMandatorySegment) {
 							haveHadSegmentBeforeMandatorySegment = true;
 						}
 						if (nextNameIsRequired && !haveHadMandatorySegment && !havePreviouslyEncounteredMandatorySegment) {
 							haveHadMandatorySegment = true;
 						}
 						haveEncounteredContent = true;
 					}
 
 				} else {
 
 					// Check if we are configured to force the encoding of this
 					// segment
 					boolean encodeEmptySegments = parserConfiguration.determineForcedEncodeIncludesTerserPath(nextTerserPath);
 					String segString = encode((Segment) rep, encodingChars, parserConfiguration, nextTerserPath);
 					if (segString.length() >= 4 || encodeEmptySegments) {
 						result.append(segString);
 
 						if (segString.length() == 3) {
 							result.append(encodingChars.getFieldSeparator());
 						}
 
 						result.append(SEGMENT_DELIMITER);
 
 						haveEncounteredContent = true;
 
 						if (nextNameIsRequired) {
 							haveHadMandatorySegment = true;
 						}
 
 						if (!haveHadMandatorySegment && !haveEncounteredMandatorySegment) {
 							haveHadSegmentBeforeMandatorySegment = true;
 						}
 
 					}
 
 				}
 
 			}
 
 		}
 
 		if (firstMandatorySegmentName != null && !haveHadMandatorySegment && !haveHadSegmentBeforeMandatorySegment && haveEncounteredContent && parserConfiguration.isEncodeEmptyMandatorySegments()) {
 			return firstMandatorySegmentName.substring(0, 3) + encodingChars.getFieldSeparator() + SEGMENT_DELIMITER + result;
 		} else {
 			return result.toString();
 		}
 	}
 
 	/**
 	 * Convenience factory method which returns an instance that has a new
 	 * {@link DefaultHapiContext} initialized with a {@link NoValidation
 	 * NoValidation validation context}.
      *
      * @return PipeParser with disabled validation
 	 */
 	public static PipeParser getInstanceWithNoValidation() {
 		HapiContext context = new DefaultHapiContext();
 		context.setValidationContext(ValidationContextFactory.noValidation());
 		return new PipeParser(context);
 	}
 
     /**
      * Returns given segment serialized as a pipe-encoded string.
      *
      * @param source segment to be encoded
      * @param encodingChars encoding characters to be used
      * @return encoded group
      */
 	public static String encode(Segment source, EncodingCharacters encodingChars) {
 		return encode(source, encodingChars, source.getMessage().getParser().getParserConfiguration(), null);
 	}
 
 	private static String encode(Segment source, EncodingCharacters encodingChars, ParserConfiguration parserConfig, String currentTerserPath) {
 		StringBuilder result = new StringBuilder();
 		result.append(source.getName());
 		result.append(encodingChars.getFieldSeparator());
 
 		// start at field 2 for MSH segment because field 1 is the field
 		// delimiter
 		int startAt = 1;
 		if (isDelimDefSegment(source.getName()))
 			startAt = 2;
 
 		// loop through fields; for every field delimit any repetitions and add
 		// field delimiter after ...
 		int numFields = source.numFields();
 
 		int forceUpToFieldNum = 0;
 		if (parserConfig != null && currentTerserPath != null) {
 			forceUpToFieldNum = parserConfig.determineForcedFieldNumForTerserPath(currentTerserPath);
 		}
 		numFields = Math.max(numFields, forceUpToFieldNum);
 
 		for (int i = startAt; i <= numFields; i++) {
 
 			String nextFieldTerserPath = currentTerserPath + "-" + i;
 			if (parserConfig != null && currentTerserPath != null) {
 				for (String nextPath : parserConfig.getForcedEncode()) {
 					if (nextPath.startsWith(nextFieldTerserPath + "-")) {
 						try {
 							source.getField(i, 0);
 						} catch (HL7Exception e) {
 							log.error("Error while encoding segment: ", e);
 						}
 					}
 				}
 			}
 
 			try {
 				Type[] reps = source.getField(i);
 				for (int j = 0; j < reps.length; j++) {
 					String fieldText = encode(reps[j], encodingChars, parserConfig, nextFieldTerserPath);
 					// if this is MSH-2, then it shouldn't be escaped, so
 					// unescape it again
 					if (isDelimDefSegment(source.getName()) && i == 2)
 						fieldText = parserConfig.getEscaping().unescape(fieldText, encodingChars);
 					result.append(fieldText);
 					if (j < reps.length - 1)
 						result.append(encodingChars.getRepetitionSeparator());
 				}
 			} catch (HL7Exception e) {
 				log.error("Error while encoding segment: ", e);
 			}
 			result.append(encodingChars.getFieldSeparator());
 		}
 
 		// strip trailing delimiters ...
 		char fieldSeparator = encodingChars.getFieldSeparator();
 		String retVal = stripExtraDelimiters(result.toString(), fieldSeparator);
 
 		int offset = isDelimDefSegment(source.getName()) ? 1 : 0;
 		while (forceUpToFieldNum > 0 && (countInstancesOf(retVal, fieldSeparator) + offset) < forceUpToFieldNum) {
 			retVal = retVal + fieldSeparator;
 		}
 
 		return retVal;
 	}
 
 	private static int countInstancesOf(String theString, char theCharToSearchFor) {
 		int retVal = 0;
 		for (int i = 0; i < theString.length(); i++) {
 			if (theString.charAt(i) == theCharToSearchFor) {
 				retVal++;
 			}
 		}
 		return retVal;
 	}
 
 	/**
 	 * Removes leading whitespace from the given string. This method was created
 	 * to deal with frequent problems parsing messages that have been
 	 * hand-written in windows. The intuitive way to delimit segments is to hit
 	 * <ENTER> at the end of each segment, but this creates both a carriage
 	 * return and a line feed, so to the parser, the first character of the next
 	 * segment is the line feed.
      *
      * @param in input string
      * @return string with leading whitespaces removed
 	 */
 	public static String stripLeadingWhitespace(String in) {
 		StringBuilder out = new StringBuilder();
 		char[] chars = in.toCharArray();
 		int c = 0;
 		while (c < chars.length) {
 			if (!Character.isWhitespace(chars[c]))
 				break;
 			c++;
 		}
 		for (int i = c; i < chars.length; i++) {
 			out.append(chars[i]);
 		}
 		return out.toString();
 	}
 
 	/**
 	 * <p>
 	 * Returns a minimal amount of data from a message string, including only
 	 * the data needed to send a response to the remote system. This includes
 	 * the following fields:
 	 * <ul>
 	 * <li>field separator</li>
 	 * <li>encoding characters</li>
 	 * <li>processing ID</li>
 	 * <li>message control ID</li>
 	 * </ul>
 	 * This method is intended for use when there is an error parsing a message,
 	 * (so the Message object is unavailable) but an error message must be sent
 	 * back to the remote system including some of the information in the
 	 * inbound message. This method parses only that required information,
 	 * hopefully avoiding the condition that caused the original error. The
 	 * other fields in the returned MSH segment are empty.
 	 * </p>
 	 */
 	public Segment getCriticalResponseData(String message) throws HL7Exception {
 		// try to get MSH segment
 		int locStartMSH = message.indexOf("MSH");
 		if (locStartMSH < 0)
 			throw new HL7Exception("Couldn't find MSH segment in message: " + message, ErrorCode.SEGMENT_SEQUENCE_ERROR);
 		int locEndMSH = message.indexOf('\r', locStartMSH + 1);
 		if (locEndMSH < 0)
 			locEndMSH = message.length();
 		String mshString = message.substring(locStartMSH, locEndMSH);
 
 		// find out what the field separator is
 		char fieldSep = mshString.charAt(3);
 
 		// get field array
 		String[] fields = split(mshString, String.valueOf(fieldSep));
 
 		try {
 			// parse required fields
 			String encChars = fields[1];
 			char compSep = encChars.charAt(0);
 			String messControlID = fields[9];
 			String[] procIDComps = split(fields[10], String.valueOf(compSep));
 
 			// fill MSH segment
 			String version = null;
 			try {
 				version = getVersion(message);
 			} catch (Exception e) { /* use the default */
 			}
 
 			if (version == null) {
 				Version availableVersion = Version.highestAvailableVersionOrDefault();
 				version = availableVersion.getVersion();
 			}
 
 			Segment msh = Parser.makeControlMSH(version, getFactory());
 			Terser.set(msh, 1, 0, 1, 1, String.valueOf(fieldSep));
 			Terser.set(msh, 2, 0, 1, 1, encChars);
 			Terser.set(msh, 10, 0, 1, 1, messControlID);
 			Terser.set(msh, 11, 0, 1, 1, procIDComps[0]);
 			Terser.set(msh, 12, 0, 1, 1, version);
 			return msh;
 
 		} catch (Exception e) {
 			throw new HL7Exception("Can't parse critical fields from MSH segment (" + e.getClass().getName() + ": " + e.getMessage() + "): " + mshString, ErrorCode.REQUIRED_FIELD_MISSING, e);
 		}
 
 	}
 
 	/**
 	 * For response messages, returns the value of MSA-2 (the message ID of the
 	 * message sent by the sending system). This value may be needed prior to
 	 * main message parsing, so that (particularly in a multi-threaded scenario)
 	 * the message can be routed to the thread that sent the request. We need
 	 * this information first so that any parse exceptions are thrown to the
 	 * correct thread. Returns null if MSA-2 can not be found (e.g. if the
 	 * message is not a response message).
 	 */
 	public String getAckID(String message) {
 		String ackID = null;
 		int startMSA = message.indexOf("\rMSA");
 		if (startMSA >= 0) {
 			int startFieldOne = startMSA + 5;
 			char fieldDelim = message.charAt(startFieldOne - 1);
 			int start = message.indexOf(fieldDelim, startFieldOne) + 1;
 			int end = message.indexOf(fieldDelim, start);
 			int segEnd = message.indexOf(SEGMENT_DELIMITER, start);
 			if (segEnd > start && segEnd < end)
 				end = segEnd;
 
 			// if there is no field delim after MSH-2, need to go to end of
 			// message, but not including end seg delim if it exists
 			if (end < 0) {
 				if (message.charAt(message.length() - 1) == '\r') {
 					end = message.length() - 1;
 				} else {
 					end = message.length();
 				}
 			}
 			if (start > 0 && end > start) {
 				ackID = message.substring(start, end);
 			}
 		}
 		log.trace("ACK ID: {}", ackID);
 		return ackID;
 	}
 
 	/**
 	 * Defaults to <code>false</code>
 	 * 
 	 * @see #isLegacyMode()
 	 * @deprecated This will be removed in HAPI 3.0
 	 */
 	public void setLegacyMode(boolean legacyMode) {
 		this.myLegacyMode = legacyMode;
 	}
 
 	/**
 	 * {@inheritDoc }
 	 */
 	@Override
 	public String encode(Message source) throws HL7Exception {
 		if (myLegacyMode != null && myLegacyMode) {
 
 			@SuppressWarnings("deprecation")
 			OldPipeParser oldPipeParser = new OldPipeParser(getFactory());
 
 			return oldPipeParser.encode(source);
 		}
 		return super.encode(source);
 	}
 
 	/**
 	 * {@inheritDoc }
 	 */
 	@Override
 	public Message parse(String message) throws HL7Exception {
 		if (myLegacyMode != null && myLegacyMode) {
 
 			@SuppressWarnings("deprecation")
 			OldPipeParser oldPipeParser = new OldPipeParser(getFactory());
 
 			return oldPipeParser.parse(message);
 		}
 		return super.parse(message);
 	}
 
 	/**
 	 * <p>
 	 * Returns <code>true</code> if legacy mode is on.
 	 * </p>
 	 * <p>
 	 * Prior to release 1.0, when an unexpected segment was encountered in a
 	 * message, HAPI would recurse to the deepest nesting in the last group it
 	 * encountered after the current position in the message, and deposit the
 	 * segment there. This could lead to unusual behaviour where all segments
 	 * afterward would not be in an expected spot within the message.
 	 * </p>
 	 * <p>
 	 * This should normally be set to false, but any code written before the
 	 * release of HAPI 1.0 which depended on this behaviour might need legacy
 	 * mode to be set to true.
 	 * </p>
 	 * <p>
 	 * Defaults to <code>false</code>. Note that this method only overrides
 	 * behaviour of the {@link #parse(java.lang.String)} and
 	 * {@link #encode(ca.uhn.hl7v2.model.Message) } methods
 	 * </p>
 	 * 
 	 * @deprecated This will be removed in HAPI 3.0
 	 */
 	public boolean isLegacyMode() {
 		if (myLegacyMode == null)
 			return (Boolean.parseBoolean(System.getProperty(DEFAULT_LEGACY_MODE_PROPERTY)));
 		return this.myLegacyMode;
 	}
 
 	/**
 	 * Returns the version ID (MSH-12) from the given message, without fully
 	 * parsing the message. The version is needed prior to parsing in order to
 	 * determine the message class into which the text of the message should be
 	 * parsed.
 	 * 
 	 * @throws HL7Exception
 	 *             if the version field can not be found.
 	 */
 	public String getVersion(String message) throws HL7Exception {
 		int startMSH = message.indexOf("MSH");
 		int endMSH = message.indexOf(PipeParser.SEGMENT_DELIMITER, startMSH);
 		if (endMSH < 0)
 			endMSH = message.length();
 		String msh = message.substring(startMSH, endMSH);
 		String fieldSep;
 		if (msh.length() > 3) {
 			fieldSep = String.valueOf(msh.charAt(3));
 		} else {
 			throw new HL7Exception("Can't find field separator in MSH: " + msh, ErrorCode.UNSUPPORTED_VERSION_ID);
 		}
 
 		String[] fields = split(msh, fieldSep);
 
 		String compSep;
 		if (fields.length >= 2 && fields[1] != null && (fields[1].length() == 4 || fields[1].length() == 5)) {
 			compSep = String.valueOf(fields[1].charAt(0)); // get component separator as 1st encoding char
 		} else {
 			throw new HL7Exception("Invalid or incomplete encoding characters - MSH-2 is " + fields[1], ErrorCode.REQUIRED_FIELD_MISSING);
 		}
 
 		String version;
 		if (fields.length >= 12) {
 			String[] comp = split(fields[11], compSep);
 			if (comp.length >= 1) {
 				version = comp[0];
 			} else {
 				throw new HL7Exception("Can't find version ID - MSH.12 is " + fields[11], ErrorCode.REQUIRED_FIELD_MISSING);
 			}
 		} else if (getParserConfiguration().isAllowUnknownVersions()) {
 			return Version.highestAvailableVersionOrDefault().getVersion();
 		} else {
 			throw new HL7Exception("Can't find version ID - MSH has only " + fields.length + " fields.", ErrorCode.REQUIRED_FIELD_MISSING);
 		}
 		return version;
 	}
 
 	@Override
 	public void parse(Message message, String string) throws HL7Exception {
 		if (message instanceof AbstractSuperMessage && message.getName() == null) {
 			String structure = getStructure(string).messageStructure;
 			((AbstractSuperMessage) message).setName(structure);
 		}
 
 		message.setParser(this);
 
 		IStructureDefinition structureDef = getStructureDefinition(message);
 		MessageIterator messageIter = new MessageIterator(message, structureDef, "MSH", true);
 
 		String[] segments = split(string, SEGMENT_DELIMITER);
 
 		if (segments.length == 0) {
 			throw new HL7Exception("Invalid message content: \"" + string + "\"");
 		}
 
 		if (segments[0] == null || segments[0].length() < 4) {
 			throw new HL7Exception("Invalid message content: \"" + string + "\"");
 		}
 
 		char delim = '|';
 		String prevName = null;
 		int repNum = 1;
 		for (int i = 0; i < segments.length; i++) {
 
 			// get rid of any leading whitespace characters ...
 			if (segments[i] != null && segments[i].length() > 0 && Character.isWhitespace(segments[i].charAt(0)))
 				segments[i] = stripLeadingWhitespace(segments[i]);
 
 			// sometimes people put extra segment delimiters at end of msg ...
 			if (segments[i] != null && segments[i].length() >= 3) {
 
 				final String name;
 				if (i == 0) {
 					if (segments[i].length() < 4) {
 						throw new HL7Exception("Invalid message content: \"" + string + "\"");
 					}
 					name = segments[i].substring(0, 3);
 					delim = segments[i].charAt(3);
 				} else {
 					if (segments[i].indexOf(delim) >= 0) {
 						name = segments[i].substring(0, segments[i].indexOf(delim));
 					} else {
 						name = segments[i];
 					}
 				}
 
 				log.trace("Parsing segment {}", name);
 
 				if (name.equals(prevName)) {
 					repNum++;
 				} else {
 					repNum = 1;
 					prevName = name;
 				}
 
 				messageIter.setDirection(name);
 
 				try {
 					if (messageIter.hasNext()) {
 						Segment next = (Segment) messageIter.next();
 						parse(next, segments[i], getEncodingChars(string), repNum);
 					}
 				} catch (Error e) {
 					if (e.getCause() instanceof HL7Exception) {
 						throw (HL7Exception)e.getCause();
 					}
 					throw e;
 				}
 			}
 		}
 		
 		applySuperStructureName(message);
 	}
 
 	/**
 	 * A struct for holding a message class string and a boolean indicating
 	 * whether it was defined explicitly.
 	 */
 	private static class MessageStructure {
 		public final String messageStructure;
 		public final boolean explicitlyDefined;
 
 		public MessageStructure(String theMessageStructure, boolean isExplicitlyDefined) {
 			messageStructure = theMessageStructure;
 			explicitlyDefined = isExplicitlyDefined;
 		}
 	}
 
 	private static class Holder<T> {
 		private T myObject;
 
 		public T getObject() {
 			return myObject;
 		}
 
 		public void setObject(T theObject) {
 			myObject = theObject;
 		}
 	}
 
 }