/*
* 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.webapp.controller;
import java.io.IOException;
import java.util.*;
import com.eaglegenomics.simlims.core.SecurityProfile;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.stereotype.Controller;
import org.springframework.ui.ModelMap;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.bind.support.SessionStatus;
import org.springframework.web.servlet.ModelAndView;
import com.eaglegenomics.simlims.core.User;
import uk.ac.bbsrc.tgac.miso.core.data.type.KitType;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import uk.ac.bbsrc.tgac.miso.core.data.*;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedExperimentException;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.security.util.LimsSecurityUtils;
import uk.ac.bbsrc.tgac.miso.core.util.LimsUtils;
import uk.ac.bbsrc.tgac.miso.sqlstore.util.DbUtils;
@Controller
@RequestMapping("/experiment")
@SessionAttributes("experiment")
public class EditExperimentController {
protected static final Logger log = LoggerFactory.getLogger(EditExperimentController.class);
@Autowired
private SecurityManager securityManager;
@Autowired
private RequestManager requestManager;
@Autowired
private DataObjectFactory dataObjectFactory;
@Autowired
private JdbcTemplate interfaceTemplate;
public void setInterfaceTemplate(JdbcTemplate interfaceTemplate) {
this.interfaceTemplate = interfaceTemplate;
}
public void setDataObjectFactory(DataObjectFactory dataObjectFactory) {
this.dataObjectFactory = dataObjectFactory;
}
public void setRequestManager(RequestManager requestManager) {
this.requestManager = requestManager;
}
public void setSecurityManager(SecurityManager securityManager) {
this.securityManager = securityManager;
}
@ModelAttribute("maxLengths")
public Map<String, Integer> maxLengths() throws IOException {
return DbUtils.getColumnSizes(interfaceTemplate, "Experiment");
}
@ModelAttribute("platforms")
public Collection<Platform> populatePlatforms() throws IOException {
return requestManager.listAllPlatforms();
}
public Collection<? extends Pool> populateAvailablePools(User user, Experiment experiment) throws IOException {
if (experiment.getPlatform() != null) {
List<Pool> pools = new ArrayList<Pool>();
for (Pool p : requestManager.listAllPoolsByPlatform(experiment.getPlatform().getPlatformType())) {
if (experiment.getPool() == null || !experiment.getPool().equals(p)) {
pools.add(p);
}
Collections.sort(pools);
}
return pools;
}
return Collections.emptyList();
}
@RequestMapping(value = "/new/{studyId}", method = RequestMethod.GET)
public ModelAndView newAssignedExperiment(@PathVariable Long studyId,
ModelMap model) throws IOException {
return setupForm(AbstractExperiment.UNSAVED_ID, studyId, model);
}
@RequestMapping(value = "/rest/{experimentId}", method = RequestMethod.GET)
public @ResponseBody Experiment jsonRest(@PathVariable Long experimentId) throws IOException {
return requestManager.getExperimentById(experimentId);
}
@RequestMapping(value = "/{experimentId}", method = RequestMethod.GET)
public ModelAndView setupForm(@PathVariable Long experimentId,
ModelMap model) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Experiment experiment = requestManager.getExperimentById(experimentId);
if (experiment == null) {
throw new SecurityException("No such Experiment");
}
if (!experiment.userCanRead(user)) {
throw new SecurityException("Permission denied.");
}
model.put("formObj", experiment);
model.put("experiment", experiment);
model.put("libraryKits", experiment.getKitsByKitType(KitType.LIBRARY));
model.put("emPcrKits", experiment.getKitsByKitType(KitType.EMPCR));
model.put("clusteringKits", experiment.getKitsByKitType(KitType.CLUSTERING));
model.put("sequencingKits", experiment.getKitsByKitType(KitType.SEQUENCING));
model.put("multiplexingKits", experiment.getKitsByKitType(KitType.MULTIPLEXING));
model.put("availablePools", populateAvailablePools(user, experiment));
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, experiment, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, experiment, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, experiment, securityManager.listAllGroups()));
model.put("title", "Experiment " + experimentId);
return new ModelAndView("/pages/editExperiment.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show experiment", ex);
}
throw ex;
}
}
@RequestMapping(value = "/{experimentId}/study/{studyId}", method = RequestMethod.GET)
public ModelAndView setupForm(@PathVariable Long experimentId,
@PathVariable Long studyId,
ModelMap model) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Experiment experiment = null;
if (experimentId == AbstractExperiment.UNSAVED_ID) {
experiment = dataObjectFactory.getExperiment();
model.put("title", "New Experiment");
}
else {
experiment = requestManager.getExperimentById(experimentId);
model.put("title", "Experiment " + experimentId);
}
if (experiment == null) {
throw new SecurityException("No such Experiment");
}
if (!experiment.userCanRead(user)) {
throw new SecurityException("Permission denied.");
}
if (studyId != null) {
Study study = requestManager.getStudyById(studyId);
model.addAttribute("study", study);
experiment.setStudy(study);
if (Arrays.asList(user.getRoles()).contains("ROLE_TECH")) {
SecurityProfile sp = new SecurityProfile(user);
LimsUtils.inheritUsersAndGroups(experiment, study.getSecurityProfile());
sp.setOwner(user);
experiment.setSecurityProfile(sp);
}
else {
experiment.inheritPermissions(study);
}
}
model.put("formObj", experiment);
model.put("experiment", experiment);
model.put("libraryKits", experiment.getKitsByKitType(KitType.LIBRARY));
model.put("emPcrKits", experiment.getKitsByKitType(KitType.EMPCR));
model.put("clusteringKits", experiment.getKitsByKitType(KitType.CLUSTERING));
model.put("sequencingKits", experiment.getKitsByKitType(KitType.SEQUENCING));
model.put("multiplexingKits", experiment.getKitsByKitType(KitType.MULTIPLEXING));
model.put("availablePools", populateAvailablePools(user, experiment));
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, experiment, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, experiment, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, experiment, securityManager.listAllGroups()));
return new ModelAndView("/pages/editExperiment.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show experiment", ex);
}
throw ex;
}
}
@RequestMapping(method = RequestMethod.POST)
public String processSubmit(@ModelAttribute("experiment") Experiment experiment,
ModelMap model,
SessionStatus session) throws IOException, MalformedExperimentException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
if (!experiment.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
requestManager.saveExperiment(experiment);
session.setComplete();
model.clear();
return "redirect:/miso/experiment/" + experiment.getId();
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to save Experiment", ex);
}
throw ex;
}
}
}