Java tutorial
/* * Genoogle: Similar DNA Sequences Searching Engine and Tools. (http://genoogle.pih.bio.br) * Copyright (C) 2008,2009 Felipe Fernandes Albrecht (felipe.albrecht@gmail.com) * * For further information check the LICENSE file. */ package bio.pih.genoogle.interfaces; import java.io.ByteArrayOutputStream; import java.io.File; import java.io.IOException; import java.io.UnsupportedEncodingException; import java.security.InvalidParameterException; import java.util.Collection; import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.NoSuchElementException; import javax.annotation.Resource; import javax.jws.WebMethod; import javax.jws.WebParam; import javax.jws.WebService; import javax.servlet.http.HttpSession; import javax.xml.ws.WebServiceContext; import javax.xml.ws.WebServiceException; import javax.xml.ws.handler.MessageContext; import org.apache.log4j.Logger; import org.dom4j.Document; import org.dom4j.io.OutputFormat; import org.dom4j.io.XMLWriter; import bio.pih.genoogle.Genoogle; import bio.pih.genoogle.index.IndexConstructionException; import bio.pih.genoogle.index.ValueOutOfBoundsException; import bio.pih.genoogle.io.AbstractSequenceDataBank; import bio.pih.genoogle.io.DuplicateDatabankException; import bio.pih.genoogle.io.IndexedSequenceDataBank; import bio.pih.genoogle.io.Output; import bio.pih.genoogle.io.SplittedDatabankCollection; import bio.pih.genoogle.io.reader.ParseException; import bio.pih.genoogle.search.SearchParams; import bio.pih.genoogle.search.SearchParams.Parameter; import bio.pih.genoogle.search.results.SearchResults; import bio.pih.genoogle.seq.DNAAlphabet; import bio.pih.genoogle.seq.IllegalSymbolException; import com.google.common.collect.Lists; import com.google.common.collect.Maps; @WebService(targetNamespace = "http://webservices.interfaces.genoogle.pih.bio") public class WebServices { private static Logger logger = Logger.getLogger(WebServices.class.getName()); private static Genoogle genoogle = Genoogle.getInstance(); @Resource private WebServiceContext wsContext; @WebMethod(exclude = true) @Resource public void initializeContext(WebServiceContext wsContext) { System.out.println("Setting WebServiceContext for the Genoogle Web Services."); this.wsContext = wsContext; } @WebMethod(operationName = "name") public String name() { return Genoogle.SOFTWARE_NAME; } @WebMethod(operationName = "version") public Double version() { return Genoogle.VERSION; } @WebMethod(operationName = "databanks") public List<String> databanks() { List<String> databanksList = Lists.newLinkedList(); Collection<AbstractSequenceDataBank> databanks = genoogle.getDatabanks(); for (AbstractSequenceDataBank databank : databanks) { databanksList.add(databank.getName()); } return databanksList; } @SuppressWarnings("unchecked") @WebMethod(operationName = "parameters") public List<String> parameters() { MessageContext mc = wsContext.getMessageContext(); HttpSession session = ((javax.servlet.http.HttpServletRequest) mc.get(MessageContext.SERVLET_REQUEST)) .getSession(); if (session == null) { throw new WebServiceException("No session in WebServiceContext"); } Map<Parameter, Object> parameters = (Map<Parameter, Object>) session.getAttribute("parameters"); if (parameters == null) { parameters = SearchParams.getSearchParamsMap(); } List<String> parametersList = Lists.newLinkedList(); for (Entry<Parameter, Object> entry : parameters.entrySet()) { parametersList.add(entry.getKey().toString() + "=" + entry.getValue().toString()); } return parametersList; } @SuppressWarnings("unchecked") @WebMethod(operationName = "setParameter") public boolean setParameter(@WebParam(name = "parameter") String parameter, @WebParam(name = "value") String paramValue) { MessageContext mc = wsContext.getMessageContext(); HttpSession session = ((javax.servlet.http.HttpServletRequest) mc.get(MessageContext.SERVLET_REQUEST)) .getSession(); if (session == null) { throw new WebServiceException("No session in WebServiceContext"); } Map<Parameter, Object> parameters = (Map<Parameter, Object>) session.getAttribute("parameters"); if (parameters == null) { parameters = SearchParams.getSearchParamsMap(); } Parameter p = Parameter.getParameterByName(parameter); if (p == null) { return false; } Object value = p.convertValue(paramValue); parameters.put(p, value); session.setAttribute("parameters", parameters); return true; } @SuppressWarnings("unchecked") @WebMethod(operationName = "search") public String search(@WebParam(name = "query") String query, @WebParam(name = "databank") String databank) { MessageContext mc = wsContext.getMessageContext(); HttpSession session = ((javax.servlet.http.HttpServletRequest) mc.get(MessageContext.SERVLET_REQUEST)) .getSession(); if (session == null) { throw new WebServiceException("No session in WebServiceContext"); } Map<Parameter, Object> parameters = (Map<Parameter, Object>) session.getAttribute("parameters"); if (parameters == null) { parameters = SearchParams.getSearchParamsMap(); } SearchResults sr = genoogle.doSyncSearch(query, databank, parameters); Document doc = Output.genoogleOutputToXML(sr); return xmlToString(doc); } @SuppressWarnings("unchecked") @WebMethod(operationName = "searchWithParameters") public String searchWithParameters(@WebParam(name = "query") String query, @WebParam(name = "databank") String databank, @WebParam(name = "parametersList") List<String> parametersList) { MessageContext mc = wsContext.getMessageContext(); HttpSession session = ((javax.servlet.http.HttpServletRequest) mc.get(MessageContext.SERVLET_REQUEST)) .getSession(); if (session == null) { throw new WebServiceException("No session in WebServiceContext"); } Map<Parameter, Object> sessionParameters = (Map<Parameter, Object>) session.getAttribute("parameters"); Map<Parameter, Object> parameters = Maps.newHashMap(); if (sessionParameters != null) { for (Entry<Parameter, Object> e : sessionParameters.entrySet()) { parameters.put(e.getKey(), e.getValue()); } } for (String param : parametersList) { String[] p = param.split("="); if (p.length != 2) { throw new InvalidParameterException(param + " is invalid."); } Parameter parameterByName = Parameter.getParameterByName(p[0]); if (parameterByName == null) { throw new InvalidParameterException(p[0] + " is not a parameter name."); } // TODO: to verify, protect if the value is not possible. Object convertValue = parameterByName.convertValue(p[1]); parameters.put(parameterByName, convertValue); } SearchResults sr = genoogle.doSyncSearch(query, databank, parameters); Document doc = Output.genoogleOutputToXML(sr); return xmlToString(doc); } @WebMethod public boolean createDatabank(@WebParam(name = "name") String name, @WebParam(name = "fastaFiles") List<String> fastaFiles, @WebParam(name = "subSequenceLength") int subSequenceLength, @WebParam(name = "mask") String mask, @WebParam(name = "numberOfSubDatabanks") int numberOfSubDatabanks, @WebParam(name = "lowComplexityFilter") int lowComplexityFilter) { // TODO: check if it as at least one element File pwd = new File(fastaFiles.get(0)).getParentFile(); // TODO: get alphabet. SplittedDatabankCollection splittedSequenceDatabank = new SplittedDatabankCollection(name, DNAAlphabet.SINGLETON, pwd, subSequenceLength, numberOfSubDatabanks, mask); for (String f : fastaFiles) { File fastaFile = new File(f); // TODO: do not use IndexedSequenceDataBank to store temporary fasta file informations. IndexedSequenceDataBank databank = new IndexedSequenceDataBank(fastaFile.getName(), DNAAlphabet.SINGLETON, subSequenceLength, mask, new File(fastaFile.getName()), splittedSequenceDatabank); try { splittedSequenceDatabank.addDatabank(databank); } catch (DuplicateDatabankException e) { // TODO Auto-generated catch block e.printStackTrace(); } } try { splittedSequenceDatabank.encodeSequences(false); } catch (NoSuchElementException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ValueOutOfBoundsException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IndexConstructionException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ParseException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IllegalSymbolException e) { // TODO Auto-generated catch block e.printStackTrace(); } return true; } private String xmlToString(Document doc) { ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); OutputFormat outformat = OutputFormat.createPrettyPrint(); outformat.setTrimText(false); XMLWriter writer = null; try { writer = new XMLWriter(outputStream, outformat); } catch (UnsupportedEncodingException e) { logger.fatal(e); return e.getLocalizedMessage(); } try { writer.write(doc); } catch (IOException e) { logger.fatal(e); return e.getLocalizedMessage(); } try { return outputStream.toString("UTF-8"); } catch (UnsupportedEncodingException e) { logger.fatal(e); return e.getLocalizedMessage(); } } }