/*
* Copyright (c) 2012. The Genome Analysis Centre, Norwich, UK
* MISO project contacts: Robert Davey, Mario Caccamo @ TGAC
* *********************************************************************
*
* This file is part of MISO.
*
* MISO is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MISO is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MISO. If not, see <http://www.gnu.org/licenses/>.
*
* *********************************************************************
*/
package uk.ac.bbsrc.tgac.miso.spring.ajax;
import org.apache.commons.codec.binary.Base64;
import uk.ac.bbsrc.tgac.miso.core.data.Project;
import com.eaglegenomics.simlims.core.User;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import net.sf.json.JSONObject;
import net.sourceforge.fluxion.ajax.Ajaxified;
import net.sourceforge.fluxion.ajax.util.JSONUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.core.authority.GrantedAuthorityImpl;
import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.security.core.userdetails.UserDetails;
import org.springframework.security.ldap.userdetails.InetOrgPerson;
import uk.ac.bbsrc.tgac.miso.core.data.*;
import uk.ac.bbsrc.tgac.miso.core.data.impl.LibraryDilution;
import uk.ac.bbsrc.tgac.miso.core.data.impl.UserImpl;
import uk.ac.bbsrc.tgac.miso.core.event.Alert;
import uk.ac.bbsrc.tgac.miso.core.event.type.AlertLevel;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import uk.ac.bbsrc.tgac.miso.core.util.LimsUtils;
import javax.servlet.http.HttpSession;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
/**
* uk.ac.bbsrc.tgac.miso.miso.spring.ajax
* <p/>
* Info
*
* @author Xingdong Bian
* @author Rob Davey
* @since 0.0.2
*/
@Ajaxified
public class DashboardHelperService {
protected static final Logger log = LoggerFactory.getLogger(DashboardHelperService.class);
@Autowired
private SecurityManager securityManager;
@Autowired
private RequestManager requestManager;
public JSONObject checkUser(HttpSession session, JSONObject json) {
String username = json.getString("username");
if (username != null && !username.equals("")) {
if (SecurityContextHolder.getContext().getAuthentication().getName().equals(username)) {
try {
User user = securityManager.getUserByLoginName(username);
if (user == null) {
//user is authed, but doesn't exist in the LIMS DB. Save that user!
User u = new UserImpl();
Object o = SecurityContextHolder.getContext().getAuthentication().getPrincipal();
if (o instanceof UserDetails) {
UserDetails details = (UserDetails) o;
u.setLoginName(details.getUsername());
u.setFullName(details.getUsername());
u.setPassword(details.getPassword());
u.setActive(true);
if (details.getAuthorities().contains(new GrantedAuthorityImpl("ROLE_ADMIN"))) {
u.setAdmin(true);
}
if (details.getAuthorities().contains(new GrantedAuthorityImpl("ROLE_INTERNAL"))) {
u.setInternal(true);
u.setRoles(new String[]{"ROLE_INTERNAL"});
}
else if (details.getAuthorities().contains(new GrantedAuthorityImpl("ROLE_EXTERNAL"))) {
u.setExternal(true);
u.setRoles(new String[]{"ROLE_EXTERNAL"});
}
else {
log.warn("Unrecognised roles");
}
if (details instanceof InetOrgPerson) {
u.setFullName(((InetOrgPerson) details).getDisplayName());
u.setEmail(((InetOrgPerson) details).getMail());
}
securityManager.saveUser(u);
}
else {
return JSONUtils.SimpleJSONError("The UserDetailsService specified in the Spring config cannot support mapping of usernames to UserDetails objects");
}
}
else {
//the user isn't null, but LDAP is "newer" than the LIMS, i.e. LDAP pass changed but LIMS still the same
Object o = SecurityContextHolder.getContext().getAuthentication().getPrincipal();
if (o instanceof UserDetails) {
UserDetails details = (UserDetails) o;
if (!user.getPassword().equals(details.getPassword())) {
user.setPassword(details.getPassword());
securityManager.saveUser(user);
}
}
}
return null;
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Something went wrong trying to get user information from the database: " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("Cannot check LIMS user database table if you are not authenticated as that user!");
}
}
return JSONUtils.SimpleJSONError("Please supply a valid username to check");
}
public JSONObject searchProject(HttpSession session, JSONObject json) {
String searchStr = json.getString("str");
try {
List<Project> projects;
StringBuilder b = new StringBuilder();
if (!"".equals(searchStr)) {
projects = new ArrayList<Project>(requestManager.listAllProjectsBySearch(searchStr));
}
else {
projects = new ArrayList<Project>(requestManager.listAllProjectsWithLimit(50));
}
if (projects.size() > 0) {
Collections.sort(projects);
Collections.reverse(projects);
for (Project p : projects) {
b.append("<a class=\"dashboardresult\" href=\"/miso/project/" + p.getProjectId() + "\"><div onMouseOver=\"this.className='dashboardhighlight'\" onMouseOut=\"this.className='dashboard'\" class=\"dashboard\">");
b.append("Name: <b>" + p.getName() + "</b><br/>");
b.append("Alias: <b>" + p.getAlias() + "</b><br/>");
b.append("</div></a>");
}
}
else {
b.append("No matches");
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject searchStudy(HttpSession session, JSONObject json) {
String searchStr = json.getString("str");
try {
List<Study> studies;
StringBuilder b = new StringBuilder();
if (!"".equals(searchStr)) {
studies = new ArrayList<Study>(requestManager.listAllStudiesBySearch(searchStr));
}
else {
studies = new ArrayList<Study>(requestManager.listAllStudiesWithLimit(50));
}
if (studies.size() > 0) {
Collections.sort(studies);
Collections.reverse(studies);
for (Study s : studies) {
b.append("<a class=\"dashboardresult\" href=\"/miso/study/" + s.getId() + "\"><div onMouseOver=\"this.className='dashboardhighlight'\" onMouseOut=\"this.className='dashboard'\" class=\"dashboard\">");
b.append("Name: <b>" + s.getName() + "</b><br/>");
b.append("Alias: <b>" + s.getAlias() + "</b><br/>");
b.append("</div></a>");
}
}
else {
b.append("No matches");
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject searchExperiment(HttpSession session, JSONObject json) {
String searchStr = json.getString("str");
try {
List<Experiment> experiments;
StringBuilder b = new StringBuilder();
if (!"".equals(searchStr)) {
experiments = new ArrayList<Experiment>(requestManager.listAllExperimentsBySearch(searchStr));
}
else {
experiments = new ArrayList<Experiment>(requestManager.listAllExperimentsWithLimit(50));
}
if (experiments.size() > 0) {
Collections.sort(experiments);
Collections.reverse(experiments);
for (Experiment e : experiments) {
b.append("<a class=\"dashboardresult\" href=\"/miso/experiment/" + e.getId() + "\"><div onMouseOver=\"this.className='dashboardhighlight'\" onMouseOut=\"this.className='dashboard'\" class=\"dashboard\">");
b.append("Name: <b>" + e.getName() + "</b><br/>");
b.append("Alias: <b>" + e.getAlias() + "</b><br/>");
b.append("</div></a>");
}
}
else {
b.append("No matches");
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject searchRun(HttpSession session, JSONObject json) {
String searchStr = json.getString("str");
try {
List<Run> runs;
StringBuilder b = new StringBuilder();
if (!"".equals(searchStr)) {
runs = new ArrayList<Run>(requestManager.listAllRunsBySearch(searchStr));
}
else {
runs = new ArrayList<Run>(requestManager.listAllRunsWithLimit(50));
}
if (runs.size() > 0) {
Collections.sort(runs);
Collections.reverse(runs);
for (Run r : runs) {
b.append("<a class=\"dashboardresult\" href=\"/miso/run/" + r.getId() + "\"><div onMouseOver=\"this.className='dashboardhighlight'\" onMouseOut=\"this.className='dashboard'\" class=\"dashboard\">");
b.append("Name: <b>" + r.getName() + "</b><br/>");
b.append("Alias: <b>" + r.getAlias() + "</b><br/>");
b.append("</div></a>");
}
}
else {
b.append("No matches");
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject searchLibraryDilution(HttpSession session, JSONObject json) {
String searchStr = json.getString("str");
try {
List<LibraryDilution> libraryDilutions;
StringBuilder b = new StringBuilder();
if (!"".equals(searchStr)) {
libraryDilutions = new ArrayList<LibraryDilution>(requestManager.listAllLibraryDilutionsBySearchOnly(searchStr));
}
else {
libraryDilutions = new ArrayList<LibraryDilution>(requestManager.listAllLibraryDilutionsWithLimit(50));
}
if (libraryDilutions.size() > 0) {
Collections.sort(libraryDilutions);
Collections.reverse(libraryDilutions);
for (LibraryDilution ld : libraryDilutions) {
if (ld != null) {
if (ld.getLibrary() != null) {
b.append("<a class=\"dashboardresult\" href=\"/miso/library/" + ld.getLibrary().getId() + "\"><div onMouseOver=\"this.className='dashboardhighlight'\" onMouseOut=\"this.className='dashboard'\" class=\"dashboard\">");
b.append("Name: <b>" + ld.getName() + "</b><br/>");
b.append("From Library: <b>" + ld.getLibrary().getAlias() + "(" + ld.getLibrary().getName() + ")</b><br/>");
// b.append("From Sample: <b>" + ld.getLibrary().getSample().getAlias() + "(" + ld.getLibrary().getSample().getName() + ")</b><br/>");
b.append("</div></a>");
}
}
}
}
else {
b.append("No matches");
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject searchLibrary(HttpSession session, JSONObject json) {
String searchStr = json.getString("str");
try {
List<Library> libraries;
StringBuilder b = new StringBuilder();
if (!"".equals(searchStr)) {
if (LimsUtils.isBase64String(searchStr)) {
//Base64-encoded string, most likely a barcode image beeped in. decode and search
searchStr = new String(Base64.decodeBase64(searchStr));
}
libraries = new ArrayList<Library>(requestManager.listAllLibrariesBySearch(searchStr));
}
else {
libraries = new ArrayList<Library>(requestManager.listAllLibrariesWithLimit(50));
}
if (libraries.size() > 0) {
Collections.sort(libraries);
Collections.reverse(libraries);
for (Library l : libraries) {
b.append("<a class=\"dashboardresult\" href=\"/miso/library/" + l.getId() + "\"><div onMouseOver=\"this.className='dashboardhighlight'\" onMouseOut=\"this.className='dashboard'\" class=\"dashboard\">");
b.append("Name: <b>" + l.getName() + "</b><br/>");
b.append("Alias: <b>" + l.getAlias() + "</b><br/>");
b.append("</div></a>");
}
}
else {
b.append("No matches");
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject searchSample(HttpSession session, JSONObject json) {
String searchStr = json.getString("str");
try {
List<Sample> samples;
StringBuilder b = new StringBuilder();
if (!"".equals(searchStr)) {
if (LimsUtils.isBase64String(searchStr)) {
//Base64-encoded string, most likely a barcode image beeped in. decode and search
searchStr = new String(Base64.decodeBase64(searchStr));
}
samples = new ArrayList<Sample>(requestManager.listAllSamplesBySearch(searchStr));
}
else {
samples = new ArrayList<Sample>(requestManager.listAllSamplesWithLimit(50));
}
if (samples.size() > 0) {
Collections.sort(samples);
Collections.reverse(samples);
for (Sample s : samples) {
b.append("<a class=\"dashboardresult\" href=\"/miso/sample/" + s.getId() + "\"><div onMouseOver=\"this.className='dashboardhighlight'\" onMouseOut=\"this.className='dashboard'\" class=\"dashboard\">");
b.append("Name: <b>" + s.getName() + "</b><br/>");
b.append("Alias: <b>" + s.getAlias() + "</b><br/>");
b.append("</div></a>");
}
}
else {
b.append("No matches");
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject checkAlerts(HttpSession session, JSONObject json) {
JSONObject response = new JSONObject();
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
if (!requestManager.listUnreadAlertsByUserId(user.getUserId()).isEmpty()) {
response.put("newAlerts", true);
}
}
catch (IOException e) {
e.printStackTrace();
JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
return response;
}
public JSONObject getAlerts(HttpSession session, JSONObject json) {
StringBuilder b = new StringBuilder();
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
List<Alert> alerts;
if (json.has("showReadAlerts") && json.getBoolean("showReadAlerts")) {
alerts = new ArrayList<Alert>(requestManager.listAlertsByUserId(user.getUserId()));
}
else {
alerts = new ArrayList<Alert>(requestManager.listUnreadAlertsByUserId(user.getUserId()));
}
Collections.sort(alerts);
for (Alert a : alerts) {
if (a.getAlertLevel().equals(AlertLevel.CRITICAL) || a.getAlertLevel().equals(AlertLevel.HIGH)) {
b.append("<div alertId='" + a.getAlertId() + "' class=\"dashboard error\">");
}
else {
b.append("<div alertId='" + a.getAlertId() + "' class=\"dashboard\">");
}
b.append(a.getAlertDate() + " <b>" + a.getAlertTitle() + "</b><br/>");
b.append(a.getAlertText() + "<br/>");
if (!a.getAlertRead()) {
b.append("<span onclick='Utils.alert.confirmAlertRead(this);' class='float-right ui-icon ui-icon-circle-close'></span>");
}
b.append("</div>");
}
}
catch (IOException e) {
e.printStackTrace();
JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
public JSONObject getSystemAlerts(HttpSession session, JSONObject json) {
StringBuilder b = new StringBuilder();
long limit = 20;
if (json.has("limit")) limit = json.getLong("limit");
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
if (user.isAdmin()) {
List<Alert> alerts = new ArrayList<Alert>(requestManager.listAlertsByUserId(0L, limit));
Collections.sort(alerts);
Collections.reverse(alerts);
for (Alert a : alerts) {
if (a.getAlertLevel().equals(AlertLevel.CRITICAL) || a.getAlertLevel().equals(AlertLevel.HIGH)) {
b.append("<div alertId='" + a.getAlertId() + "' class=\"dashboard error\">");
}
else {
b.append("<div alertId='" + a.getAlertId() + "' class=\"dashboard\">");
}
b.append(a.getAlertDate() + " <b>" + a.getAlertTitle() + "</b><br/>");
b.append(a.getAlertText() + "<br/>");
b.append("</div>");
}
}
else {
JSONUtils.SimpleJSONError("Failed: You do not have access to view system level alerts");
}
}
catch (IOException e) {
e.printStackTrace();
JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
public JSONObject setAlertAsRead(HttpSession session, JSONObject json) {
Long alertId = json.getLong("alertId");
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Alert a = requestManager.getAlertById(alertId);
if (a.getAlertUser().equals(user)) {
a.setAlertRead(true);
requestManager.saveAlert(a);
}
else {
JSONUtils.SimpleJSONError("You do not have the rights to set this alert as read");
}
}
catch (IOException e) {
e.printStackTrace();
JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
return JSONUtils.SimpleJSONResponse("ok");
}
public JSONObject setAllAlertsAsRead(HttpSession session, JSONObject json) {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
List<Alert> alerts = new ArrayList<Alert>(requestManager.listUnreadAlertsByUserId(user.getUserId()));
for (Alert a : alerts) {
if (a.getAlertUser().equals(user)) {
a.setAlertRead(true);
requestManager.saveAlert(a);
}
else {
JSONUtils.SimpleJSONError("You do not have the rights to set this alert as read");
}
}
}
catch (IOException e) {
e.printStackTrace();
JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
return JSONUtils.SimpleJSONResponse("ok");
}
public JSONObject showLatestReceivedSamples(HttpSession session, JSONObject json) {
try {
StringBuilder b = new StringBuilder();
Collection<Sample> samples = requestManager.listAllSamplesByReceivedDate(100);
if (samples.size() > 0) {
for (Sample s : samples) {
if (s.getReceivedDate() != null) {
b.append("<a class=\"dashboardresult\" href=\"/miso/project/" + s.getProject().getId() + "\"><div onMouseOver=\"this.className='dashboardhighlight'\" onMouseOut=\"this.className='dashboard'\" class=\"dashboard\">");
b.append("Name: <b>" + s.getProject().getName() + "</b><br/>");
b.append("Alias: <b>" + s.getProject().getAlias() + "</b><br/>");
b.append("Last Received: <b>" + LimsUtils.getDateAsString(s.getReceivedDate()) + "</b><br/>");
b.append("</div>");
}
}
}
else {
b.append("No matches");
}
return JSONUtils.JSONObjectResponse("html", b.toString());
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public void setSecurityManager(SecurityManager securityManager) {
this.securityManager = securityManager;
}
public void setRequestManager(RequestManager requestManager) {
this.requestManager = requestManager;
}
}