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

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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.
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package de.sekmi.li2b2.services;

import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.logging.Logger;

import javax.inject.Inject;
import javax.inject.Singleton;
import javax.ws.rs.POST;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import javax.ws.rs.core.UriInfo;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.parsers.ParserConfigurationException;

import org.w3c.dom.Element;

import de.sekmi.li2b2.api.pm.ProjectManager;
import de.sekmi.li2b2.api.pm.User;
import de.sekmi.li2b2.api.pm.Project;

import de.sekmi.li2b2.hive.Credentials;
import de.sekmi.li2b2.hive.HiveException;
import de.sekmi.li2b2.hive.HiveRequest;
import de.sekmi.li2b2.hive.HiveResponse;
import de.sekmi.li2b2.hive.I2b2Constants;
import de.sekmi.li2b2.hive.pm.Cell;
import de.sekmi.li2b2.hive.pm.Param;
import de.sekmi.li2b2.hive.pm.UserProject;
import de.sekmi.li2b2.services.token.TokenManager;

@Singleton
@Path(PMService.SERVICE_URL)
public class PMService extends AbstractPMService{
	private static final Logger log = Logger.getLogger(PMService.class.getName());
	public static final String SERVICE_URL = "/i2b2/services/PMService/";

	private List otherCells;
	private ProjectManager manager;
	private TokenManager tokens;
	
	public PMService() throws HiveException{
		otherCells = new ArrayList<>(4);
		setIndentOutput(true);
		registerCell(new Cell("ONT", "OntologyService", OntologyService.SERVICE_PATH));
		registerCell(new Cell("WORK", "WorkplaceSevice", WorkplaceService.SERVICE_PATH));
		registerCell(new Cell("CRC", "QueryToolService", AbstractCRCService.SERVICE_PATH));
	}
	

	@Inject
	public void setProjectManager(ProjectManager manager){
		this.manager = manager;
	}
	@Inject
	public void setTokenManager(TokenManager manager){
		this.tokens = manager;
	}
	@Override
	public TokenManager getTokenManager(){
		return this.tokens;
	}
	public void registerCell(Cell cell){
		otherCells.add(cell);
	}

	@POST
	@Path("getServices")
	@Produces(MediaType.APPLICATION_XML)
	public Response getServices(InputStream requestBody, @Context UriInfo uri) throws HiveException, ParserConfigurationException, JAXBException{
		// Information used by the official webclient (as of v1.7.07c):
		// project/[id,role='DATA_AGG',]
		// cell_data[id,name,project_path,url], cell_data/param
		return super.handleRequest(requestBody);
	}

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

	private static void appendProject(Element parent, Project project){
//		Element el = parent.getOwnerDocument().createElementNS("","project");
		Element el = parent.getOwnerDocument().createElement("project");
		parent.appendChild(el);
		el.setAttribute("id", project.getId());
		appendTextElement(el, "name", project.getName());
//		appendTextElement(el, "key", "K_"+project.getId()); // XXX what for?
		appendTextElement(el, "wiki", "https://github.org/rwm/li2b2");
//		appendTextElement(el, "description", "About "+project.getName());
		appendTextElement(el, "path", project.getPath());
//		appendTextElement(el, "user_name", "demo"); // XXX what for?
	}

	@Override
	protected void getAllProject(HiveResponse response) {
		Element el = response.addBodyElement(I2b2Constants.PM_NS, "projects");
		el.setPrefix("ns4");
		for( Project project : manager.getProjects() ){
			appendProject(el, project);
		}
		
	}


	@Override
	protected void getProject(HiveResponse response, String projectId, String path) {
		// TODO Auto-generated method stub
		
	}


	private static void appendRole(Element parent, String project, String user, String role){
		Element el = parent.getOwnerDocument().createElement("role");
		//el.setPrefix("ns4");
		parent.appendChild(el);
		appendTextElement(el, "project_id", project);
		appendTextElement(el, "user_name", user);
		appendTextElement(el, "role", role);
	}
	private static void appendRoles(Element parent, Project project, User user){
		for( String role : project.getUserRoles(user) ){
			appendRole(parent, project.getId(), user.getName(), role);
		}		
	}
	@Override
	protected void getAllRoles(HiveResponse response, String projectId, String userId) {
		Element el = response.addBodyElement(I2b2Constants.PM_NS, "roles");
		el.setPrefix("ns4");
		if( projectId == null ){
			// roles for all projects
			if( userId == null ){
				// all projects and all users
				throw new UnsupportedOperationException("Not implemented yet");				
			}else{
				// all projects for specific users
				throw new UnsupportedOperationException("Not implemented yet");
			}
		}else{
			// roles for specific project
			Project project = manager.getProjectById(projectId);
			if( project == null ){
				// non-existing project -> no roles
			}else if( userId == null ){
				// roles for all users in the specified project
				for( User user : manager.getUsers() ){
					appendRoles(el, project, user);
				}
			}else{
				// roles for specific user in project
				User user = manager.getUserById(userId);
				if( user != null ){
					appendRoles(el, project, user);					
				}
				// otherwise: non-existing user -> no roles
			}
		}
	}


	@Override
	protected void getAllProjectParams(HiveResponse response, String projectId) {
		// TODO Auto-generated method stub
		
	}


	@Override
	protected void getAllHive(HiveResponse response) {
		// TODO Auto-generated method stub
		
	}


	@Override
	protected void getAllCells(HiveResponse response, String projectId) throws JAXBException {
		JAXBContext jaxb = JAXBContext.newInstance(Cell.class);
		Marshaller marshaller = jaxb.createMarshaller();
		marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);
		Element el = response.addBodyElement(I2b2Constants.PM_NS, "cells");
		el.setPrefix("ns4");
		for( Cell cell : otherCells ){
			marshaller.marshal(cell, el);
		}
	}


	@Override
	protected void getCell(HiveResponse response, String id, String path) {
		// TODO Auto-generated method stub
		
	}

	private void appendUser(Element parent, User user){
		// TODO compare to official response (elements and order)
		Element el = parent.getOwnerDocument().createElementNS("","user");
		parent.appendChild(el);
		appendTextElement(el, "full_name", user.getFullName());
		appendTextElement(el, "user_name", user.getName());
		appendTextElement(el, "email", "[email protected]");
		appendTextElement(el, "domain", user.getDomain());
		appendTextElement(el, "is_admin", "true");
	}

	@Override
	protected void getAllUsers(HiveResponse response) {
		Element el = response.addBodyElement(I2b2Constants.PM_NS, "users");
		el.setPrefix("ns4");
		for( User user : manager.getUsers() ){
			appendUser(el, user);
		}
	}


	@Override
	protected void getUser(HiveResponse response, String userId) {
		// TODO does the official server send a 'users' wrapper?
		Element el = response.addBodyElement(I2b2Constants.PM_NS, "users");
		el.setPrefix("ns4");
		User user = manager.getUserById(userId);
		if( user != null ){
			appendUser(el, user);
		}
	}


	@Override
	protected void getUserConfiguration(HiveRequest req, HiveResponse resp, String projectId) throws JAXBException {
		Credentials cred = req.getSecurity();
		User user;
		String sessionKey = null;
		if( cred.isToken() ){
			// need session manager
			sessionKey = cred.getPassword(); // remove SessionKey: prefix
			// TODO check for valid session
			
			user = null;
		}else if( manager != null ){
			// check user manager
			user = manager.getUserById(cred.getUser());
			if( user != null && user.hasPassword(cred.getPassword().toCharArray()) ){
				// user authenticated
				log.info("Valid user login: "+cred.getUser());
				// create session
				sessionKey = getTokenManager().registerPrincipal(cred.getUser());
			}else{
				// user or password not valid
				log.info("Invalid credentials: "+cred.getUser());
				user = null;
			}
		}else{
			user = null;
			// no user manager
		}
		if( user == null ){
			// login failed
			resp.setResultStatus("ERROR", "Authentication failed");
			return;
		}
		JAXBContext jaxb = JAXBContext.newInstance(Cell.class,UserProject.class);
		Marshaller marshaller = jaxb.createMarshaller();
		marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);

		// webclient only users configure/[full_name|is_admin], project/[name|path}
		Element el = resp.addBodyElement(I2b2Constants.PM_NS, "configure");
		appendTextElement(el, "environment", "DEVELOPMENT");
		appendTextElement(el, "helpURL", "https://github.com/rwm/li2b2");
		// user info
		// TODO namespaces are not clean, 
		Element ue = (Element)el.appendChild(el.getOwnerDocument().createElementNS("","user"));
		appendTextElement(ue, "full_name", user.getFullName());
		appendTextElement(ue, "user_name", user.getName());
		// TODO session/password
		Element p = appendTextElement(ue, "password", "SessionKey:"+sessionKey);
		p.setAttribute("is_token", Boolean.TRUE.toString());
		p.setAttribute("token_ms_timeout", Long.toString(getTokenManager().getExpirationMillis()));
		appendTextElement(ue, "domain", user.getDomain());
		appendTextElement(ue, "is_admin", "true");
		// add projects
		for( Project project : user.getProjects() ){
			// fill project
			UserProject up = new UserProject();
			up.id = project.getId();
			up.name = project.getName();
			up.path = project.getPath();
			Set roles = project.getUserRoles(user);
			up.role = new String[roles.size()];
			roles.toArray(up.role);
			// param demo
			up.params = new Param[]{
					// TODO allow configuration of announcements by project manager
					new Param("announcement","This is a demo of the li2b2 server."),
					new Param("Software","li2b2 server")
			};
			// append
			marshaller.marshal(up, ue);
		}
		appendTextElement(el, "domain_name", cred.getDomain());
		appendTextElement(el, "domain_id", "i2b2");
		appendTextElement(el, "active", "true");

		// add cells
		Element cells = (Element)el.appendChild(el.getOwnerDocument().createElementNS("","cell_datas"));
		for( Cell cell : otherCells ){
			marshaller.marshal(cell, cells);
		}
		// TODO remove xmlns="" from elements 'user', 'cell_datas' (which was needed for JAXB)
		
//		for( Cell cell : this.otherCells ){
//			marshaller.marshal(cell, cells);
//		}
	}


	@Override
	protected void setPassword(HiveResponse response, Credentials cred, String newPassword) {
		User user = manager.getUserById(cred.getUser());
		if( user == null ){
			response.setResultStatus("ERROR", "User not found");
		}
		user.setPassword(newPassword.toCharArray());
	}


	@Override
	protected void setProject(HiveResponse response, String id, String name, String key, String wiki,
			String description, String path) {
		Project project = manager.getProjectById(id);
		if( project == null ){
			// create project
			manager.addProject(id, name);
		}else{
			// TODO set path
		}
		// TODO set other attributes
		appendResponseText(response, "1 records");
	}

	// TODO use this method
	private boolean verifyAdmin(HiveRequest request){
		String name = getAuthenticatedUser(request);
		if( name == null ){
			return false;
		}
		User user = manager.getUserById(name);
		if( user != null && user.isAdmin() ){
			return true;
		}else{
			return false;
		}
	}

	@Override
	protected void setUser(HiveResponse response, String userId, String fullName, String email, boolean admin,
			String password) {
		// verify that the current user has admin privileges
		User user = manager.getUserById(userId);
		if( user == null ){
			user = manager.addUser(userId);
		}
		// TODO set other attributes
		user.setPassword(password.toCharArray());
		appendResponseText(response, "1 records");
	}


	@Override
	protected void setRole(HiveResponse response, String userId, String role, String projectId) {
		User user = manager.getUserById(userId);
		Project project = manager.getProjectById(projectId);
		if( user == null || project == null ){
			response.setResultStatus("ERROR", "Project or user not found");
			return;
		}
		// TODO some roles will automatically remove other roles because only one role per group is active
		// e.g. one of MANAGER/USER,  
		// e.g. one of DATA_OBFSC/DATA_LDS/DATA_AGG/DATA_DEID/DATA_PROT
		project.getUserRoles(user).add(role);
		log.info("Role added for project "+projectId+": "+userId+" -> "+role);
		log.info("Current roles: "+project.getUserRoles(user).toString());
		appendResponseText(response, "1 records");
	}


	private void appendResponseText(HiveResponse response, String text){
		Element el = response.addBodyElement(I2b2Constants.PM_NS, "response");
		el.setPrefix("ns4");
		el.setTextContent(text);
	}
	@Override
	protected void deleteRole(HiveResponse response, String userId, String role, String projectId) {
		User user = manager.getUserById(userId);
		Project project = manager.getProjectById(projectId);
		if( user == null || project == null ){
			response.setResultStatus("ERROR", "Project or user not found");
			return;
		}
		project.getUserRoles(user).remove(role);
		log.info("Role removed for project "+projectId+": "+userId+" -> "+role);
		log.info("Remaining roles: "+project.getUserRoles(user).toString());
		// TODO error if role not there
		appendResponseText(response, "1 records");
	}


	@Override
	protected void deleteUser(HiveResponse response, String userId) {
		if( manager.getUserById(userId) == null ){
			// return same result status as the original server
			response.setResultStatus("ERROR", "User not updated, does it exist?");
		}
		manager.deleteUser(userId);
		appendResponseText(response, "1 records");
	}
}