/*
* 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 com.eaglegenomics.simlims.core.SecurityProfile;
import com.eaglegenomics.simlims.core.User;
import org.springframework.validation.BindException;
import uk.ac.bbsrc.tgac.miso.core.data.type.PlatformType;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedDilutionException;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedExperimentException;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
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 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.illumina.IlluminaPool;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedLibraryException;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.factory.TgacDataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.security.util.LimsSecurityUtils;
import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
import java.util.*;
/**
* com.eaglegenomics.miso.web
* <p/>
* Info
*
* @author Rob Davey
* @since 0.0.2
*/
@Controller
@RequestMapping("/pool/illumina")
@SessionAttributes("pool")
public class EditIlluminaPoolController {
protected static final Logger log = LoggerFactory.getLogger(EditIlluminaPoolController.class);
@Autowired
private SecurityManager securityManager;
@Autowired
private RequestManager requestManager;
@Autowired
private DataObjectFactory dataObjectFactory;
public void setDataObjectFactory(DataObjectFactory dataObjectFactory) {
this.dataObjectFactory = dataObjectFactory;
}
public void setRequestManager(RequestManager requestManager) {
this.requestManager = requestManager;
}
public void setSecurityManager(SecurityManager securityManager) {
this.securityManager = securityManager;
}
private List<? extends Dilution> populateAvailableDilutions(Pool pool) throws IOException {
ArrayList<LibraryDilution> libs = new ArrayList<LibraryDilution>();
for (Dilution l : requestManager.listAllLibraryDilutionsByPlatform(PlatformType.ILLUMINA)) {
if (!pool.getDilutions().contains(l)) {
libs.add((LibraryDilution)l);
}
}
Collections.sort(libs);
return libs;
}
public Collection<Experiment> populateExperiments(Long experimentId, Pool p) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Collection<Experiment> es = new ArrayList<Experiment>();
for (Experiment e : requestManager.listAllExperiments()) {
if (e.getPlatform().getPlatformType().equals(p.getPlatformType())) {
if (experimentId != null) {
if (e.getId() != experimentId) {
es.add(e);
}
}
else {
es.add(e);
}
}
}
return es;
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to list experiments", ex);
}
throw ex;
}
}
@RequestMapping(value = "/new", method = RequestMethod.GET)
public ModelAndView newUnassignedIlluminaPool(ModelMap model) throws IOException {
return setupForm(AbstractPool.UNSAVED_ID, model);
}
@RequestMapping(value = "/new/{experimentId}", method = RequestMethod.GET)
public ModelAndView newAssignedIlluminaPool(@PathVariable Long experimentId, ModelMap model) throws IOException {
return setupFormWithExperiment(AbstractPool.UNSAVED_ID, experimentId, model);
}
@RequestMapping(value = "/{poolId}", method = RequestMethod.GET)
public ModelAndView setupForm(@PathVariable Long poolId,
ModelMap model) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Pool pool = null;
if (poolId == AbstractPool.UNSAVED_ID) {
pool = dataObjectFactory.getIlluminaPool(user);
model.put("title", "New Illumina Pool");
}
else {
pool = requestManager.getPoolById(poolId);
model.put("title", "Illumina Pool "+poolId);
}
if (pool == null) {
throw new SecurityException("No such Illumina Pool");
}
if (!pool.userCanRead(user)) {
throw new SecurityException("Permission denied.");
}
model.put("formObj", pool);
model.put("pool", pool);
model.put("availableDilutions", populateAvailableDilutions(pool));
model.put("accessibleExperiments", populateExperiments(null, pool));
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, pool, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, pool, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, pool, securityManager.listAllGroups()));
return new ModelAndView("/pages/editIlluminaPool.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show Illumina pool", ex);
}
throw ex;
}
}
@RequestMapping(value = "/{poolId}/experiment/{experimentId}", method = RequestMethod.GET)
public ModelAndView setupFormWithExperiment(@PathVariable Long poolId,
@PathVariable Long experimentId,
ModelMap model) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Pool<? extends Poolable> pool = null;
if (poolId == AbstractPool.UNSAVED_ID) {
pool = dataObjectFactory.getPool(user);
pool.setPlatformType(PlatformType.ILLUMINA);
model.put("title", "New Illumina Pool");
}
else {
pool = requestManager.getPoolById(poolId);
model.put("title", "Illumina Pool "+poolId);
}
if (pool == null) {
throw new SecurityException("No such Illumina Pool");
}
if (!pool.userCanRead(user)) {
throw new SecurityException("Permission denied.");
}
if (experimentId != null) {
model.put("accessibleExperiments", populateExperiments(experimentId, pool));
}
else {
model.put("accessibleExperiments", populateExperiments(null, pool));
}
model.put("formObj", pool);
model.put("pool", pool);
model.put("availableDilutions", populateAvailableDilutions(pool));
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, pool, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, pool, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, pool, securityManager.listAllGroups()));
return new ModelAndView("/pages/editIlluminaPool.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show Illumina pool", ex);
}
throw ex;
}
// catch (MalformedExperimentException e) {
// e.printStackTrace();
// throw new IOException(e);
// }
}
@RequestMapping(value = "/new/dilution/{dilutionId}", method = RequestMethod.GET)
public ModelAndView setupFormWithDilution(@PathVariable Long dilutionId,
ModelMap model) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
IlluminaPool pool = dataObjectFactory.getIlluminaPool(user);
model.put("title", "New Illumina Pool");
if (pool == null) {
throw new SecurityException("No such Illumina Pool");
}
if (!pool.userCanRead(user)) {
throw new SecurityException("Permission denied.");
}
if (dilutionId != null) {
LibraryDilution ld = requestManager.getLibraryDilutionById(dilutionId);
if (ld != null) {
pool.addPoolableElement(ld);
}
}
model.put("formObj", pool);
model.put("pool", pool);
model.put("availableDilutions", populateAvailableDilutions(pool));
model.put("accessibleExperiments", populateExperiments(null, pool));
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, pool, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, pool, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, pool, securityManager.listAllGroups()));
return new ModelAndView("/pages/editIlluminaPool.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show Illumina pool", ex);
}
throw ex;
}
catch (MalformedDilutionException e) {
e.printStackTrace();
throw new IOException(e);
}
}
@RequestMapping(value = "/import", method = RequestMethod.POST)
public String importLibraryDilutionsToPool(HttpServletRequest request, ModelMap model) throws IOException {
IlluminaPool p = (IlluminaPool)model.get("pool");
String[] dils = request.getParameterValues("importdilslist");
for (String s : dils) {
LibraryDilution ld = requestManager.getLibraryDilutionByBarcode(s);
if (ld != null) {
try {
p.addPoolableElement(ld);
}
catch (MalformedDilutionException e) {
log.debug("Cannot add library dilution "+s+" to pool " + p.getName());
e.printStackTrace();
}
}
}
requestManager.savePool(p);
return "redirect:/miso/pool/illumina/" + p.getId();
}
@RequestMapping(method = RequestMethod.POST)
public String processSubmit(@ModelAttribute("pool") Pool pool,
ModelMap model,
SessionStatus session) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
if (!pool.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
requestManager.savePool(pool);
session.setComplete();
model.clear();
return "redirect:/miso/pool/illumina/" + pool.getId();
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to save Illumina pool", ex);
}
throw ex;
}
}
}