de.sekmi.li2b2.services.AbstractCRCService Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of li2b2-server Show documentation
This project emulates the core components of an i2b2 server backend. Basic functionality of PM, CRC, ONT and WORK cells allows the official i2b2 webclient to connect ot this emulated server.
The newest version!
package de.sekmi.li2b2.services;

import java.util.logging.Logger;

import javax.xml.XMLConstants;
import javax.xml.bind.JAXBException;
import javax.xml.parsers.ParserConfigurationException;

import org.w3c.dom.DOMException;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;

import de.sekmi.li2b2.hive.HiveException;
import de.sekmi.li2b2.hive.HiveRequest;
import de.sekmi.li2b2.hive.crc.CrcResponse;

public abstract class AbstractCRCService extends AbstractService{

	private static final Logger log = Logger.getLogger(AbstractCRCService.class.getName());
	public static final String SERVICE_PATH="/i2b2/services/QueryToolService/";

	public AbstractCRCService() throws HiveException {
		super();
		// TODO Auto-generated constructor stub
	}
	protected void handleRequest(HiveRequest req, Element crc_header, Element request, CrcResponse resp) throws HiveException, ParserConfigurationException{
		// TODO might have pdo_header instead of psm_header, add PDO support later (e.g. for timeline)
		log.info("crc header type: "+ crc_header.getLocalName());
		
		// get request type
		NodeList nl = crc_header.getElementsByTagName("request_type");
		String type = null;
		if( nl.getLength() != 0 ){
			type = nl.item(0).getTextContent();
		}
		
		// check authentication
		String userId = getAuthenticatedUser(req);
		if( userId == null ) {
			// invalid credentials
			resp.setResultStatus("ERROR", "Illegal credentials");
		}else try {
			request(userId, type, crc_header, request, resp);
		} catch (DOMException | JAXBException e) {
			resp.setResultStatus("ERROR", e.toString());
		}
	}
	protected CrcResponse createResponse(HiveRequest request) throws ParserConfigurationException{
		CrcResponse resp = new CrcResponse(createResponse(newDocumentBuilder()));
		fillResponseHeader(resp, request);
		return resp;
	}


	private void request(String userId, String type, Element psm_header, Element request, CrcResponse response) throws DOMException, JAXBException{
		String rtype = null;
		if( request != null ){
			rtype = request.getAttributeNS(XMLConstants.W3C_XML_SCHEMA_INSTANCE_NS_URI, "type");
		}
		log.info("Request:"+type+" type="+rtype);
		if( type.equals("CRC_QRY_getResultType") ){
			getResultType(response);
		}else if( type.equals("CRC_QRY_getQueryMasterList_fromUserId") ){
			String subtype = request.getLocalName();
			log.info("getQueryMasterList_fromUserId subtype="+subtype);
			if( subtype.contentEquals("request") ) {
				// list queries
				getQueryMasterList_fromUserId(response, request.getFirstChild().getTextContent());
			}else if( subtype.contentEquals("get_name_info") ) {
				// filter query list by name/content
				// TODO parse filter options from 'request' by string
				getQueryMasterList_fromUserId(response, request.getFirstChild().getTextContent());
			}
		}else if( type.equals("CRC_QRY_runQueryInstance_fromQueryDefinition") ){
			// TODO
			Node qd = request.getFirstChild();
			Node rd = request.getLastChild();
			if( qd == null || qd.getNodeType() != Node.ELEMENT_NODE || !qd.getNodeName().equals("query_definition")
					|| rd == null || rd.getNodeType() != Node.ELEMENT_NODE || !rd.getNodeName().equals("result_output_list") )
			{
				// illegal/unexpected request content
				// TODO return error
			}else{
				runQueryInstance_fromQueryDefinition(response, psm_header, (Element)qd, (Element)rd);
			}
		}else if( type.equals("CRC_QRY_deleteQueryMaster") ){
			// get master id
			String masterId = request.getElementsByTagName("query_master_id").item(0).getTextContent();
			// request also contains user id, but this is redundant and we don't need it
			deleteQueryMaster(response, masterId);
		}else if( type.equals("CRC_QRY_renameQueryMaster") ){
			// get master id
			String masterId = request.getElementsByTagName("query_master_id").item(0).getTextContent();
			String queryName = request.getElementsByTagName("query_name").item(0).getTextContent();
			// request also contains user id, but this is redundant and we don't need it
			renameQueryMaster(response, masterId, queryName);
		}else if( type.equals("CRC_QRY_getRequestXml_fromQueryMasterId") ){
			String masterId = request.getElementsByTagName("query_master_id").item(0).getTextContent();
			getRequestXml_fromQueryMasterId(response, masterId);
		}else if( type.equals("CRC_QRY_getQueryInstanceList_fromQueryMasterId") ){
			String masterId = request.getElementsByTagName("query_master_id").item(0).getTextContent();
			getQueryInstanceList_fromQueryMasterId(response, masterId);
		}else if( type.equals("CRC_QRY_getQueryResultInstanceList_fromQueryInstanceId") ){
			String instanceId = request.getElementsByTagName("query_instance_id").item(0).getTextContent();
			getQueryResultInstanceList_fromQueryInstanceId(response, instanceId);
		}else if( type.equals("CRC_QRY_getResultDocument_fromResultInstanceId") ){
			String resultInstanceId = request.getElementsByTagName("query_result_instance_id").item(0).getTextContent();
			getResultDocument_fromResultInstanceId(response, resultInstanceId);
		}else{
			// TODO 
			response.setResultStatus("ERROR", "Feature not supported (yet)");
		}
	}

	@Override
	public String getCellId() {
		return "CRC";
	}

	protected abstract void getResultType(CrcResponse response) throws JAXBException;
	protected abstract void getQueryMasterList_fromUserId(CrcResponse response, String userId) throws JAXBException;
	/**
	 * Run the specified query
	 * @param response response returned to the client
	 * @param psm_header supplied PSM header
	 * @param query_definition {@code query_definition} element
	 * @param result_output_list {@code result_output_list} element
	 * @throws JAXBException JAXP parsing error
	 */
	protected abstract void runQueryInstance_fromQueryDefinition(CrcResponse response, Element psm_header, Element query_definition, Element result_output_list)throws JAXBException;
	protected abstract void getRequestXml_fromQueryMasterId(CrcResponse response, String masterId);
	protected abstract void deleteQueryMaster(CrcResponse response, String masterId);
	protected abstract void renameQueryMaster(CrcResponse response, String masterId, String newName);
	protected abstract void getQueryInstanceList_fromQueryMasterId(CrcResponse response, String masterId);
	protected abstract void getQueryResultInstanceList_fromQueryInstanceId(CrcResponse response, String instanceId);
	protected abstract void getResultDocument_fromResultInstanceId(CrcResponse response, String resultInstancId);
}