Java tutorial
/** * <!-- LICENSE_TEXT_START --> * Copyright 2008,2009 NGIT. This software was developed in conjunction * with the National Cancer Institute, and so to the extent government * employees are co-authors, any rights in such works shall be subject * to Title 17 of the United States Code, section 105. * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the disclaimer of Article 3, * below. 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. * 2. The end-user documentation included with the redistribution, * if any, must include the following acknowledgment: * "This product includes software developed by NGIT and the National * Cancer Institute." If no such end-user documentation is to be * included, this acknowledgment shall appear in the software itself, * wherever such third-party acknowledgments normally appear. * 3. The names "The National Cancer Institute", "NCI" and "NGIT" must * not be used to endorse or promote products derived from this software. * 4. This license does not authorize the incorporation of this software * into any third party proprietary programs. This license does not * authorize the recipient to use any trademarks owned by either NCI * or NGIT * 5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED 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 NATIONAL CANCER INSTITUTE, * NGIT, OR THEIR AFFILIATES 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. * <!-- LICENSE_TEXT_END --> */ /** * SimpleSearchUtils (uses LexEVSAPI 6.1 SearchExtension) * * @author kimong * */ package gov.nih.nci.evs.browser.utils; import java.util.*; import java.util.HashSet; import java.util.Set; import java.util.StringTokenizer; import org.apache.log4j.*; import org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference; import org.LexGrid.LexBIG.Exceptions.LBException; import org.LexGrid.LexBIG.Extensions.Generic.CodingSchemeReference; import org.LexGrid.LexBIG.Extensions.Generic.SearchExtension; //import org.LexGrid.LexBIG.Impl.function.LexBIGServiceTestCase; //import org.LexGrid.LexBIG.Impl.testUtility.ServiceHolder; import org.LexGrid.LexBIG.LexBIGService.LexBIGService; import org.LexGrid.LexBIG.Utility.Iterators.ResolvedConceptReferencesIterator; import org.LexGrid.LexBIG.DataModel.Collections.*; import org.LexGrid.LexBIG.DataModel.Core.*; import org.LexGrid.LexBIG.LexBIGService.*; import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.*; import org.LexGrid.LexBIG.Utility.*; import org.LexGrid.concepts.*; import org.LexGrid.LexBIG.DataModel.InterfaceElements.*; import org.LexGrid.LexBIG.Utility.Iterators.*; import org.LexGrid.codingSchemes.*; import org.apache.log4j.*; import org.LexGrid.LexBIG.DataModel.Core.types.*; import org.LexGrid.naming.*; import org.LexGrid.LexBIG.Extensions.Generic.*; import org.apache.commons.codec.language.*; import org.LexGrid.LexBIG.Extensions.Generic.SearchExtension; public class SimpleSearchUtils { private static Logger _logger = Logger.getLogger(SimpleSearchUtils.class); final static String testID = "SearchExtensionImplTest"; public static final int BY_CODE = 1; public static final int BY_NAME = 2; public static final String EXACT_MATCH = "exactMatch"; public static final String STARTS_WITH = "startsWith"; public static final String CONTAINS = "contains"; public static final String LUCENE = "lucene"; public static final String NAMES = "names"; public static final String CODES = "codes"; public static final String PROPERTIES = "properties"; public static final String RELATIONSHIPS = "relationships"; private static String charactersToRemove = ",./\\`\"+*=@#$%^&?!"; private static String charactersTreatedAsWhitespace = "-;(){}[]<>|"; public SimpleSearchUtils() { } public ResolvedConceptReferencesIteratorWrapper search(Vector<String> schemes, Vector<String> versions, String matchText, String algorithm, String target) throws LBException { if (algorithm == null || target == null) return null; if (algorithm.compareToIgnoreCase(EXACT_MATCH) == 0 && target.compareToIgnoreCase(CODES) == 0) { return search(schemes, versions, matchText, BY_CODE, "exactMatch"); } else if (algorithm.compareToIgnoreCase(LUCENE) == 0 && target.compareToIgnoreCase(CODES) == 0) { return search(schemes, versions, matchText, BY_CODE, "exactMatch"); } else if (algorithm.compareToIgnoreCase(LUCENE) == 0 && target.compareToIgnoreCase(NAMES) == 0) { return search(schemes, versions, matchText, BY_NAME, "lucene"); } else if (algorithm.compareToIgnoreCase(CONTAINS) == 0 && target.compareToIgnoreCase(NAMES) == 0) { return search(schemes, versions, matchText, BY_NAME, "contains"); } return null; } public String preprocessingString(String input) { if (input == null) return null; StringBuffer buf = new StringBuffer(); for (int i = 0; i < input.length(); i++) { //char c = input.charAt(i); String ch = input.substring(i, i + 1); if (charactersTreatedAsWhitespace.indexOf(ch) > 0) { buf.append(" "); } else if (charactersToRemove.indexOf(ch) == -1) { buf.append(ch); } } return buf.toString(); } public static boolean isSimpleSearchSupported(String algorithm, String target) { //if (!isSearchExtensionAvaliable) return false; if (algorithm == null || target == null) return false; if (algorithm.compareToIgnoreCase(EXACT_MATCH) == 0 && target.compareToIgnoreCase(CODES) == 0) { return true; } else if (algorithm.compareToIgnoreCase(EXACT_MATCH) == 0 && target.compareToIgnoreCase(NAMES) == 0) { return true; } else if (algorithm.compareToIgnoreCase(LUCENE) == 0 && target.compareToIgnoreCase(CODES) == 0) { return true; } else if (algorithm.compareToIgnoreCase(LUCENE) == 0 && target.compareToIgnoreCase(NAMES) == 0) { return true; } else if (algorithm.compareToIgnoreCase(CONTAINS) == 0 && target.compareToIgnoreCase(NAMES) == 0) { return true; } return false; } public static boolean isSearchExtensionAvaliable() { if (getSearchExtension() == null) return false; return true; } public static SearchExtension getSearchExtension() { SearchExtension searchExtension = null; try { LexBIGService lbSvc = new RemoteServerUtil().createLexBIGService(); if (lbSvc == null) { _logger.warn("createLexBIGService returns NULL???"); return null; } searchExtension = (SearchExtension) lbSvc.getGenericExtension("SearchExtension"); return searchExtension; } catch (Exception e) { _logger.warn("SearchExtension is not available."); return null; } } public static boolean searchAllSources(String source) { if (source != null && source.compareTo("ALL") != 0) return false; return true; } public ResolvedConceptReferencesIteratorWrapper search(String scheme, String version, String matchText, int searchOption, String algorithm) throws LBException { if (scheme == null) return null; Vector<String> schemes = new Vector(); Vector<String> versions = new Vector(); schemes.add(scheme); versions.add(version); return search(schemes, versions, matchText, searchOption, algorithm); } private void printNumberOfMatches(ResolvedConceptReferencesIterator iterator) { if (iterator == null) { System.out.println("Iterator is null"); return; } try { int numRemaining = iterator.numberRemaining(); System.out.println("Number of matches: " + numRemaining); } catch (Exception ex) { ex.printStackTrace(); } } public ResolvedConceptReferencesIteratorWrapper search(Vector<String> schemes, Vector<String> versions, String matchText, int searchOption, String algorithm) throws LBException { System.out.println("search by " + matchText + ", algorithm: " + algorithm); if (schemes == null || versions == null) return null; if (schemes.size() != versions.size()) return null; if (schemes.size() == 0) return null; if (matchText == null) return null; if (searchOption != BY_CODE && searchOption != BY_NAME) return null; if (searchOption != BY_CODE && algorithm == null) return null; LexBIGService lbSvc = new RemoteServerUtil().createLexBIGService(); if (lbSvc == null) { return null; } SearchExtension searchExtension = null; try { searchExtension = (SearchExtension) lbSvc.getGenericExtension("SearchExtension"); } catch (Exception e) { _logger.warn("SearchExtension is not available."); return null; } Set<CodingSchemeReference> includes = new HashSet(); for (int i = 0; i < schemes.size(); i++) { String scheme = (String) schemes.elementAt(i); String version = (String) versions.elementAt(i); System.out.println("\t" + scheme + " (" + version + ")"); CodingSchemeReference ref = new CodingSchemeReference(); ref.setCodingScheme(scheme); if (version != null) { CodingSchemeVersionOrTag versionOrTag = new CodingSchemeVersionOrTag(); versionOrTag.setVersion(version); } includes.add(ref); } ResolvedConceptReferencesIterator iterator = null; try { iterator = searchExtension.search(matchText, includes, converToMatchAlgorithm(searchOption, algorithm)); printNumberOfMatches(iterator); } catch (Exception ex) { ex.printStackTrace(); } if (iterator != null) { return new ResolvedConceptReferencesIteratorWrapper(iterator); } return null; } protected static void displayRef(ResolvedConceptReference ref) { System.out.println(ref.getConceptCode() + ":" + ref.getEntityDescription().getContent()); } public static void dumpIterator(ResolvedConceptReferencesIterator itr) { try { while (itr.hasNext()) { try { ResolvedConceptReference[] refs = itr.next(100).getResolvedConceptReference(); for (ResolvedConceptReference ref : refs) { displayRef(ref); } } catch (Exception ex) { break; } } } catch (Exception ex) { ex.printStackTrace(); } } public static SearchExtension.MatchAlgorithm converToMatchAlgorithm(int searchOption, String algorithm) { if (algorithm == null) return null; if (searchOption != BY_CODE && searchOption != BY_NAME) return null; if (searchOption == BY_NAME) { if (algorithm.compareTo("exactMatch") == 0) { return SearchExtension.MatchAlgorithm.PRESENTATION_EXACT; } else if (algorithm.compareTo("contains") == 0) { return SearchExtension.MatchAlgorithm.PRESENTATION_CONTAINS; } else if (algorithm.compareTo("lucene") == 0) { return SearchExtension.MatchAlgorithm.LUCENE; } } else if (algorithm.compareTo("exactMatch") == 0 && searchOption == BY_CODE) { return SearchExtension.MatchAlgorithm.CODE_EXACT; } return null; } public static void main(String[] args) { boolean searchExtensionAvaliable = isSearchExtensionAvaliable(); if (!searchExtensionAvaliable) { System.out.println("SearchExtension is not available."); System.exit(1); } SimpleSearchUtils test = new SimpleSearchUtils(); try { Vector<String> schemes = new Vector(); Vector<String> versions = new Vector(); schemes.add("NCI_Thesaurus"); //versions.add("12.05d"); versions.add("13.03d"); schemes.add("NCI Metathesaurus"); versions.add("201105"); String matchText = "cell aging"; ResolvedConceptReferencesIteratorWrapper wrapper = test.search(schemes, versions, matchText, SimpleSearchUtils.BY_NAME, "contains"); if (wrapper != null) { ResolvedConceptReferencesIterator iterator = wrapper.getIterator(); if (iterator != null) { try { int numRemaining = iterator.numberRemaining(); System.out.println("Number of matches: " + numRemaining); dumpIterator(iterator); } catch (Exception ex) { ex.printStackTrace(); } } } else { System.out.println("wrapper is NULL??? " + matchText); } } catch (Exception ex) { ex.printStackTrace(); } } }