/**
 * 
 */
package oboannotator.application;

import java.io.IOException;
import java.util.ArrayList;

import oboannotator.util.AppConfig;
import oboannotator.util.Util;


/**
 * @author ahmedabdeenhamed
 *
 */
public class UserCustomedAEApplication {	
	public static void composePrimitiveAE(String dictName, String addUpdateFlag) throws IOException{
		//System.out.println("addUpdateFlag : " + addUpdateFlag);
		
		StringBuilder xmlEngineBuilder = new StringBuilder("<?xml version=\"1.0\" encoding=\"utf-8\" ?> \n");
		xmlEngineBuilder.append("<taeDescription xmlns=\"http://uima.apache.org/resourceSpecifier\"> \n");
		xmlEngineBuilder.append("	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>\n");
		xmlEngineBuilder.append("	<primitive>true</primitive>\n");
		xmlEngineBuilder.append("	<annotatorImplementationName>org.apache.uima.conceptMapper.ConceptMapper</annotatorImplementationName>\n");
		xmlEngineBuilder.append("	<analysisEngineMetaData>\n");
		xmlEngineBuilder.append("		<name>ConceptMapper</name>\n");
		xmlEngineBuilder.append("		<description></description>\n");
		xmlEngineBuilder.append("		<version>1</version>\n");
		xmlEngineBuilder.append("		<vendor></vendor>\n");
		xmlEngineBuilder.append("		<configurationParameters>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>caseMatch</name>\n");
		xmlEngineBuilder.append("			<description>desc goes here</description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>true</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>Stemmer</name>\n");
		xmlEngineBuilder.append("			<description>desc goes here</description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>ResultingAnnotationName</name>\n");
		xmlEngineBuilder.append("			<description>\n");
		xmlEngineBuilder.append("				Name of the annotation type created by this TAE,\n");
		xmlEngineBuilder.append("			</description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>true</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>ResultingEnclosingSpanName</name>\n");
		xmlEngineBuilder.append("			<description>\n");
		xmlEngineBuilder.append("				Name of the feature in the resultingAnnotation to\n");
		xmlEngineBuilder.append("			</description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>AttributeList</name>\n");
		xmlEngineBuilder.append("			<description>\n");
		xmlEngineBuilder.append("				List of attribute names for XML dictionary entry\n");
		xmlEngineBuilder.append("			</description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>true</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>true</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>FeatureList</name>\n");
		xmlEngineBuilder.append("			<description>\n");
		xmlEngineBuilder.append("				List of feature names for CAS annotation - must\n");
		xmlEngineBuilder.append("				correspond to AttributeList\n");
		xmlEngineBuilder.append("			</description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>true</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>true</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");		
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>TokenAnnotation</name>\n");
		xmlEngineBuilder.append("			<description></description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>true</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>TokenClassFeatureName</name>\n");
		xmlEngineBuilder.append("			<description>\n");
		xmlEngineBuilder.append("				Name of feature used when doing lookups against\n");
		xmlEngineBuilder.append("				IncludedTokenClasses and ExcludedTokenClasses\n");
		xmlEngineBuilder.append("			</description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>TokenTextFeatureName</name>\n");
		xmlEngineBuilder.append("			<description></description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>SpanFeatureStructure</name>\n");
		xmlEngineBuilder.append("			<description>\n");
		xmlEngineBuilder.append("				Type of annotation which corresponds to spans of\n");
		xmlEngineBuilder.append("				oboannotator.resources.data for processing (e.g. a Sentence)\n");
		xmlEngineBuilder.append("			</description>\n");
		xmlEngineBuilder.append("			<type>String</type>\n");
		xmlEngineBuilder.append("			<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>true</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");		
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>OrderIndependentLookup</name>\n");
		xmlEngineBuilder.append("			<description>\n");
		xmlEngineBuilder.append("				True if should ignore element order during lookup\n");
		xmlEngineBuilder.append("				(i.e., \"top box\" would equal \"box top\"). Default is\n");
		xmlEngineBuilder.append("				False.\n");
		xmlEngineBuilder.append("			</description>\n");
		xmlEngineBuilder.append("			<type>Boolean</type>\n");
		xmlEngineBuilder.append("			<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("			<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("		</configurationParameter>\n");
		xmlEngineBuilder.append("		<configurationParameter>\n");
		xmlEngineBuilder.append("			<name>TokenTypeFeatureName</name>\n");
		xmlEngineBuilder.append("			<description>\n");
		xmlEngineBuilder.append("				Name of feature used when doing lookups against\n");
		xmlEngineBuilder.append("				IncludedTokenTypes and ExcludedTokenTypes\n");
		xmlEngineBuilder.append("				</description>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append(				"<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>IncludedTokenTypes</name>\n");
		xmlEngineBuilder.append("				<description>\n");
		xmlEngineBuilder.append("					Type of tokens to include in lookups (if not\n");
		xmlEngineBuilder.append("					supplied, then all types are included except those\n");
		xmlEngineBuilder.append("					specifically mentioned in ExcludedTokenTypes)\n");
		xmlEngineBuilder.append("				</description>\n");
		xmlEngineBuilder.append("				<type>Integer</type>\n");
		xmlEngineBuilder.append("				<multiValued>true</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>ExcludedTokenTypes</name>\n");
		xmlEngineBuilder.append("				<description></description>\n");
		xmlEngineBuilder.append("				<type>Integer</type>\n");
		xmlEngineBuilder.append("				<multiValued>true</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>ExcludedTokenClasses</name>\n");
		xmlEngineBuilder.append("				<description>\n");
		xmlEngineBuilder.append("					Class of tokens to exclude from lookups (if not\n");
		xmlEngineBuilder.append("					supplied, then all classes are excluded except those\n");
		xmlEngineBuilder.append("					specifically mentioned in IncludedTokenClasses,\n");
		xmlEngineBuilder.append("					unless IncludedTokenClasses is not supplied, in\n");
		xmlEngineBuilder.append("					which case none are excluded)\n");
		xmlEngineBuilder.append("				</description>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>true</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>IncludedTokenClasses</name>\n");
		xmlEngineBuilder.append("				<description>\n");
		xmlEngineBuilder.append("					Class of tokens to include in lookups (if not\n");
		xmlEngineBuilder.append("					supplied, then all classes are included except those\n");
		xmlEngineBuilder.append("					specifically mentioned in ExcludedTokenClasses)\n");
		xmlEngineBuilder.append("				</description>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>true</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>TokenClassWriteBackFeatureNames</name>\n");
		xmlEngineBuilder.append("				<description>\n");
		xmlEngineBuilder.append("					names of features that should be written back to a\n");
		xmlEngineBuilder.append("					token, such as a POS tag\n");
		xmlEngineBuilder.append("				</description>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>true</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>ResultingAnnotationMatchedTextFeature</name>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>PrintDictionary</name>\n");
		xmlEngineBuilder.append("				<type>Boolean</type>\n");
		xmlEngineBuilder.append("				<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>SearchStrategy</name>\n");
		xmlEngineBuilder.append("				<description>\n");
		xmlEngineBuilder.append("				</description>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>StopWords</name>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>true</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>FindAllMatches</name>\n");
		xmlEngineBuilder.append("				<type>Boolean</type>\n");
		xmlEngineBuilder.append("				<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>MatchedTokensFeatureName</name>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>ReplaceCommaWithAND</name>\n");
		xmlEngineBuilder.append("				<type>Boolean</type>\n");
		xmlEngineBuilder.append("				<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>TokenizerDescriptorPath</name>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>true</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("			<configurationParameter>\n");
		xmlEngineBuilder.append("				<name>LanguageID</name>\n");
		xmlEngineBuilder.append("				<type>String</type>\n");
		xmlEngineBuilder.append("				<multiValued>false</multiValued>\n");
		xmlEngineBuilder.append("				<mandatory>false</mandatory>\n");
		xmlEngineBuilder.append("			</configurationParameter>\n");
		xmlEngineBuilder.append("		</configurationParameters>\n");
		xmlEngineBuilder.append("		<configurationParameterSettings>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>caseMatch</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("				<string>ignoreall</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>AttributeList</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<array>\n");
		xmlEngineBuilder.append("						<string>canonical</string>\n");
		xmlEngineBuilder.append("					</array>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>FeatureList</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<array>\n");
		xmlEngineBuilder.append("						<string>DictCanon</string>\n");
		xmlEngineBuilder.append("					</array>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>TokenAnnotation</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<string>uima.tt.TokenAnnotation</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>ResultingAnnotationName</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<string>\n");
		xmlEngineBuilder.append("						org.apache.uima.conceptMapper.DictTerm\n");
		xmlEngineBuilder.append("					</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>SpanFeatureStructure</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<string>uima.tcas.DocumentAnnotation</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>OrderIndependentLookup</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<boolean>false</boolean>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>TokenClassWriteBackFeatureNames</name>\n");
		xmlEngineBuilder.append("						<value>\n");
		xmlEngineBuilder.append("					<array />\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>IncludedTokenClasses</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<array />\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>PrintDictionary</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<boolean>false</boolean>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>FindAllMatches</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<boolean>false</boolean>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>StopWords</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<array />\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>ReplaceCommaWithAND</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<boolean>false</boolean>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>TokenizerDescriptorPath</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<string>\n");
		xmlEngineBuilder.append("						" + AppConfig.PRIMITIVE_AE_DIR + "OffsetTokenizer.xml\n");
		xmlEngineBuilder.append("					</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>ResultingEnclosingSpanName</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<string>enclosingSpan</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>MatchedTokensFeatureName</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<string>matchedTokens</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>ResultingAnnotationMatchedTextFeature</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<string>matchedText</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>SearchStrategy</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<string>ContiguousMatch</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("			<nameValuePair>\n");
		xmlEngineBuilder.append("				<name>LanguageID</name>\n");
		xmlEngineBuilder.append("				<value>\n");
		xmlEngineBuilder.append("					<string>en</string>\n");
		xmlEngineBuilder.append("				</value>\n");
		xmlEngineBuilder.append("			</nameValuePair>\n");
		xmlEngineBuilder.append("		</configurationParameterSettings>\n");
		xmlEngineBuilder.append("		<typeSystemDescription>\n");
		xmlEngineBuilder.append("			<imports>\n");
		xmlEngineBuilder.append("				<import name=\"org.apache.uima.conceptMapper.DictTerm\" />\n");
		xmlEngineBuilder.append("			<import\n");
		xmlEngineBuilder.append("				name=\"org.apache.uima.conceptMapper.support.tokenizer.TokenAnnotation\" />\n");
		xmlEngineBuilder.append("			</imports>\n");
		xmlEngineBuilder.append("			<types>\n");
		xmlEngineBuilder.append("			<typeDescription>\n");
		xmlEngineBuilder.append("				<name>uima.tt.TokenAnnotation</name>\n");
		xmlEngineBuilder.append("				<description></description>\n");
		xmlEngineBuilder.append("				<supertypeName>uima.tcas.Annotation</supertypeName>\n");
		xmlEngineBuilder.append("				<features>\n");
		xmlEngineBuilder.append("					<featureDescription>\n");
		xmlEngineBuilder.append("						<name>SemClass</name>\n");
		xmlEngineBuilder.append("						<description>\n");
		xmlEngineBuilder.append("							semantic class of token\n");
		xmlEngineBuilder.append("						</description>\n");
		xmlEngineBuilder.append("						<rangeTypeName>\n");
		xmlEngineBuilder.append("							uima.cas.String\n");
		xmlEngineBuilder.append("						</rangeTypeName>\n");
		xmlEngineBuilder.append("					</featureDescription>\n");
		xmlEngineBuilder.append("					<featureDescription>\n");
		xmlEngineBuilder.append("						<name>POS</name>\n");
		xmlEngineBuilder.append("						<description>\n");
		xmlEngineBuilder.append("							Part of SPeech of term to which this\n");
		xmlEngineBuilder.append("								token is a part\n");
		xmlEngineBuilder.append("						</description>\n");
		xmlEngineBuilder.append("						<rangeTypeName>\n");
		xmlEngineBuilder.append("							uima.cas.String\n");
		xmlEngineBuilder.append("						</rangeTypeName>\n");
		xmlEngineBuilder.append("					</featureDescription>\n");
		xmlEngineBuilder.append("					<featureDescription>\n");
		xmlEngineBuilder.append("						<name>frost_TokenType</name>\n");
		xmlEngineBuilder.append("						<description></description>\n");
		xmlEngineBuilder.append("						<rangeTypeName>\n");
		xmlEngineBuilder.append("							uima.cas.Integer\n");
		xmlEngineBuilder.append("						</rangeTypeName>\n");
		xmlEngineBuilder.append("					</featureDescription>\n");
		xmlEngineBuilder.append("				</features>\n");
		xmlEngineBuilder.append("			</typeDescription>\n");
		xmlEngineBuilder.append("		</types>\n");
		xmlEngineBuilder.append("	</typeSystemDescription>\n");
		xmlEngineBuilder.append("	<typePriorities>\n");
		xmlEngineBuilder.append("		<priorityList>\n");
		xmlEngineBuilder.append("				<type>uima.tt.TokenAnnotation</type>\n");
		xmlEngineBuilder.append("				</priorityList>\n");
		xmlEngineBuilder.append("</typePriorities>\n");
		xmlEngineBuilder.append("	<fsIndexCollection />\n");
		xmlEngineBuilder.append("	<capabilities>\n");
		xmlEngineBuilder.append("		<capability>\n");
		xmlEngineBuilder.append("			<inputs>\n");
		xmlEngineBuilder.append("				<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("					uima.tt.TokenAnnotation\n");
		xmlEngineBuilder.append("				</type>\n");
		xmlEngineBuilder.append("				<!-- <type allAnnotatorFeatures=\"true\">uima.tt.SentenceAnnotation</type>\n");
		xmlEngineBuilder.append("					<type allAnnotatorFeatures=\"true\">uima.tt.ParagraphAnnotation</type> -->\n");
		xmlEngineBuilder.append("			</inputs>\n");
		xmlEngineBuilder.append("			<outputs>\n");
		xmlEngineBuilder.append("			<!-- \n");
		xmlEngineBuilder.append("				<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("					org.apache.uima.conceptMapper.DictTerm\n");
		xmlEngineBuilder.append("				</type>\n");
		xmlEngineBuilder.append("				<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("					uima.tt.TokenAnnotation\n");
		xmlEngineBuilder.append("				</type>\n");
		xmlEngineBuilder.append("				<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("					org.apache.uima.conceptMapper.support.tokenizer.TokenAnnotation\n");
		xmlEngineBuilder.append("				</type>\n");
		xmlEngineBuilder.append("				<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("					uima.tcas.DocumentAnnotation\n");
		xmlEngineBuilder.append("				</type>  -->\n");
		xmlEngineBuilder.append("			</outputs>\n");
		xmlEngineBuilder.append("			<languagesSupported />\n");
		xmlEngineBuilder.append("		</capability>\n");
		xmlEngineBuilder.append("	</capabilities>\n");
		xmlEngineBuilder.append("	<operationalProperties>\n");
		xmlEngineBuilder.append("		<modifiesCas>true</modifiesCas>\n");
		xmlEngineBuilder.append("		<multipleDeploymentAllowed>true</multipleDeploymentAllowed>\n");
		xmlEngineBuilder.append("		<outputsNewCASes>false</outputsNewCASes>\n");
		xmlEngineBuilder.append("	</operationalProperties>\n");
		xmlEngineBuilder.append("</analysisEngineMetaData>\n");
		xmlEngineBuilder.append("<externalResourceDependencies>\n");
		xmlEngineBuilder.append("	<externalResourceDependency>\n");
		xmlEngineBuilder.append("			<key>DictionaryFile</key>\n");
		xmlEngineBuilder.append("		<description>dictionary file loader.</description>\n");
		xmlEngineBuilder.append("		<interfaceName>\n");
		xmlEngineBuilder.append("			org.apache.uima.conceptMapper.support.dictionaryResource.DictionaryResource\n");
		xmlEngineBuilder.append("		</interfaceName>\n");
		xmlEngineBuilder.append("		<optional>false</optional>\n");
		xmlEngineBuilder.append("	</externalResourceDependency>\n");
		xmlEngineBuilder.append("</externalResourceDependencies>\n");
		xmlEngineBuilder.append("<resourceManagerConfiguration>\n");
		xmlEngineBuilder.append("	<externalResources>\n");
		xmlEngineBuilder.append("		<externalResource>\n");
		if(addUpdateFlag.equals(AppConfig.ADD_NEW_DICTION)){
			xmlEngineBuilder.append("			<name>" + Util.removeFileExtension(dictName) +"Dictionary</name>\n");
		}else if(addUpdateFlag.equals(AppConfig.UPDATE_DICTION)){
			xmlEngineBuilder.append("			<name>" + Util.removeFileExtension(dictName) +"Dictionary</name>\n");
		}
		xmlEngineBuilder.append("			<description>\n");
		xmlEngineBuilder.append("				A file containing the dictionary. Modify this URL to\n");
		xmlEngineBuilder.append("				use a different dictionary.\n");
		xmlEngineBuilder.append("			</description>\n");
		xmlEngineBuilder.append("			<fileResourceSpecifier>\n");
		
		if(addUpdateFlag.equals(AppConfig.ADD_NEW_DICTION)){
			xmlEngineBuilder.append("				<fileUrl>file:" +  AppConfig.DICTIONARY_DIR+ dictName + AppConfig.XML_EXTENSION + "</fileUrl>\n");
		}else if(addUpdateFlag.equals(AppConfig.UPDATE_DICTION)){			
			//System.out.println("Valid dict name in the descreptor: " + Util.removeString(dictName, "AE.xml"));
			xmlEngineBuilder.append("				<fileUrl>file:" +  AppConfig.DICTIONARY_DIR+ Util.removeString(dictName, "AE.xml")+ "</fileUrl>\n");
			//return;
		}
		xmlEngineBuilder.append("			</fileResourceSpecifier>\n");
		xmlEngineBuilder.append("			<implementationName>\n");
		xmlEngineBuilder.append("				org.apache.uima.conceptMapper.support.dictionaryResource.DictionaryResource_impl\n");
		xmlEngineBuilder.append("			</implementationName>\n");
		xmlEngineBuilder.append("		</externalResource>\n");
		xmlEngineBuilder.append("	</externalResources>\n");
		xmlEngineBuilder.append("	<externalResourceBindings>\n");
		xmlEngineBuilder.append("		<externalResourceBinding>\n");
		xmlEngineBuilder.append("			<key>DictionaryFile</key>\n");
		if(addUpdateFlag.equals(AppConfig.ADD_NEW_DICTION)){
			xmlEngineBuilder.append("			<resourceName>" + Util.removeFileExtension(dictName) +"Dictionary</resourceName>\n");
		}else if(addUpdateFlag.equals(AppConfig.UPDATE_DICTION)){
			xmlEngineBuilder.append("			<resourceName>" + Util.removeFileExtension(dictName) +"Dictionary</resourceName>\n");
		}			
		xmlEngineBuilder.append("		</externalResourceBinding>\n");
		xmlEngineBuilder.append("	</externalResourceBindings>\n");
		xmlEngineBuilder.append("</resourceManagerConfiguration>\n");
		xmlEngineBuilder.append("</taeDescription>\n");
		
		//String primitiveEngineXmlContent = xmlEngineBuilder.toString();
		//composePrimitiveAE(String dictDir, String dictName, String primAEDir)
		if(addUpdateFlag.equals(AppConfig.ADD_NEW_DICTION)){
			Util.writeStringToFile(xmlEngineBuilder.toString(), AppConfig.DICTIONARY_AE_DIR,  dictName+AppConfig.AE_STRING+AppConfig.XML_EXTENSION);
		}else if(addUpdateFlag.equals(AppConfig.UPDATE_DICTION)){
			//System.out.println("Dict name before saving to file: " + dictName);
			//Util.writeStringToFile(xmlEngineBuilder.toString(), AppConfig.DICTIONARY_AE_DIR,  dictName);
		}
	}

	public static void composeAggregateAE(ArrayList<String> dictionariesList) throws IOException{
		StringBuilder xmlEngineBuilder = new StringBuilder();				
		xmlEngineBuilder.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
		xmlEngineBuilder.append("<taeDescription xmlns=\"http://uima.apache.org/resourceSpecifier\">\n");
		xmlEngineBuilder.append("	<frameworkImplementation>\n");
		xmlEngineBuilder.append("		org.apache.uima.java\n");
		xmlEngineBuilder.append("	</frameworkImplementation>\n");
		xmlEngineBuilder.append("	<primitive>false</primitive>\n");
		xmlEngineBuilder.append("	<delegateAnalysisEngineSpecifiers>\n");	
		
		
		xmlEngineBuilder.append("		<delegateAnalysisEngine key=\"MedlineDocument\">\n");
		xmlEngineBuilder.append("			<import location=\"../primitive/MedlineDocumentAnnotatorAE.xml\"/>\n");
		xmlEngineBuilder.append("		</delegateAnalysisEngine>\n");

		xmlEngineBuilder.append("		<delegateAnalysisEngine key=\"MedlineField\">\n");
		xmlEngineBuilder.append("			<import location=\"../primitive/MedlineFieldAnnotatorAE.xml\"/>\n");
		xmlEngineBuilder.append("		</delegateAnalysisEngine>\n");
		
		xmlEngineBuilder.append("		<delegateAnalysisEngine key=\"OpenNLPTokenizer\">\n");
		xmlEngineBuilder.append("			<import location=\"../../../../../opennlp_wrappers/descriptors/OpenNLPAggregate.xml\"/>\n");
		xmlEngineBuilder.append("		</delegateAnalysisEngine>\n");
		
		xmlEngineBuilder.append("		<delegateAnalysisEngine key=\"Tokenizer\">\n");
		xmlEngineBuilder.append("			<import location=\"../primitive/OffsetTokenizer.xml\" />\n");
		xmlEngineBuilder.append("		</delegateAnalysisEngine>\n");				
		
		for(String currentDictionary: dictionariesList){
			xmlEngineBuilder.append("		<delegateAnalysisEngine key=\""+ Util.removeFileExtension(currentDictionary) + "ConceptMapper\">\n");
			xmlEngineBuilder.append("			<import location=\"../dictionary/"+ currentDictionary + "\"" +  " />\n");
			xmlEngineBuilder.append("		</delegateAnalysisEngine>\n");
		}

		
		xmlEngineBuilder.append("	</delegateAnalysisEngineSpecifiers>\n");
		xmlEngineBuilder.append("	<analysisEngineMetaData>\n");
		xmlEngineBuilder.append("		<name>DictMatcher</name>\n");
		xmlEngineBuilder.append("		<configurationParameters />\n");
		xmlEngineBuilder.append("		<configurationParameterSettings />\n");
		xmlEngineBuilder.append("		<flowConstraints>\n");
		xmlEngineBuilder.append("			<fixedFlow>\n");
		xmlEngineBuilder.append("				<node>MedlineDocument</node>\n");
		xmlEngineBuilder.append("				<node>MedlineField</node>\n");
		xmlEngineBuilder.append("				<node>OpenNLPTokenizer</node>\n");
		xmlEngineBuilder.append("				<node>Tokenizer</node>\n");
		//<node>MedlineDocument</node>
		//<node>MedlineField</node>
		//<node>MedlineField</node>

		for(String dictDescriptor: dictionariesList){			
			xmlEngineBuilder.append("				<node>" + Util.removeFileExtension(dictDescriptor) + "ConceptMapper" + "</node>\n");
		}		

		xmlEngineBuilder.append("			</fixedFlow>\n");
		xmlEngineBuilder.append("		</flowConstraints>\n");
		xmlEngineBuilder.append("		<fsIndexCollection />\n");
		xmlEngineBuilder.append("		<capabilities>\n");
		xmlEngineBuilder.append("			<capability>\n");
		xmlEngineBuilder.append("				<inputs>\n");
	 	xmlEngineBuilder.append("					<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("						oboannotator.typesys.MedlineDocument</type>\n");
		xmlEngineBuilder.append("					<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("						oboannotator.typesys.MedlineField</type>\n");		
		xmlEngineBuilder.append("				</inputs>\n");		
		xmlEngineBuilder.append("				<outputs>\n");
	 	xmlEngineBuilder.append("					<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("						oboannotator.typesys.MedlineDocument</type>\n");
		xmlEngineBuilder.append("					<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("						oboannotator.typesys.MedlineField</type>\n");	
		xmlEngineBuilder.append("					<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("						org.apache.uima.examples.opennlp.Token</type>\n");		
		xmlEngineBuilder.append("					<type allAnnotatorFeatures=\"true\">\n");
		xmlEngineBuilder.append("						org.apache.uima.conceptMapper.DictTerm\n");
		xmlEngineBuilder.append("					</type>\n");
		xmlEngineBuilder.append("				</outputs>\n");
		xmlEngineBuilder.append("				<languagesSupported />\n");
		xmlEngineBuilder.append("			</capability>\n");
		xmlEngineBuilder.append("		</capabilities>\n");
		xmlEngineBuilder.append("		<operationalProperties>\n");
		xmlEngineBuilder.append("			<modifiesCas>true</modifiesCas>\n");
		xmlEngineBuilder.append("			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>\n");
		xmlEngineBuilder.append("		</operationalProperties>\n");
		xmlEngineBuilder.append("	</analysisEngineMetaData>\n");
		xmlEngineBuilder.append("</taeDescription>\n");
		
		//System.out.println("AppConfig.AGGREGATE_AE_DIR: " + AppConfig.AGGREGATE_AE_DIR);
		//System.out.println("AppConfig.USER_ASSEMBLED_AGGREGATE_AE: " + AppConfig.USER_ASSEMBLED_AGGREGATE_AE);
		
		
		Util.writeStringToFile(xmlEngineBuilder.toString(), AppConfig.AGGREGATE_AE_DIR, AppConfig.USER_ASSEMBLED_AGGREGATE_AE);	
	}
		
	/**
	 * @param args
	 */
	public static void main(String[] args) {
		//System.out.println("creating the AE...");
		
		
		//String aggAEDir = "/Users/ahmedabdeenhamed/Projects/concept-mapper-project/oboannotator.resources.descriptors/analysis_engine/aggregate/";
		String dictDir = "src/oboannotator.resources.descriptors/analysis_engine/dictionary/";
		ArrayList<String> list = new ArrayList<String>();
		list.add("EnvoAE.xml");
		//list.add("GazAE.xml");
		
//		String dictDir = "/Users/ahmedabdeenhamed/Projects/concept-mapper-project/oboannotator.resources/dict/";
		//String dictName = "testDict.xml";
		
		try {
			//UserCustomedAEApplication.composePrimitiveAE("newDictionary", "UPDATE_DICTIONARY");
			//composeAggregateAE(list, dictDir, aggAEDir, aggAEName)			
			UserCustomedAEApplication.composeAggregateAE(list);
		} catch (IOException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}

	}

}