/*
* 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 org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.*;
import com.eaglegenomics.simlims.core.ActivitySessionFactory;
import com.eaglegenomics.simlims.core.manager.ProtocolManager;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
//import com.eaglegenomics.simlims.spring.ActivityControllerHelper;
import uk.ac.bbsrc.tgac.miso.webapp.util.ActivityControllerHelperLoader;
@Controller
@SessionAttributes({"activitySession", "dataModel"})
public class EditActivityController {
protected static final Logger log = LoggerFactory.getLogger(EditActivityController.class);
//@Autowired
private InputDataXmlView inputDataXmlView;
//@Autowired
private ActivityControllerHelperLoader activityControllerHelperLoader;
//@Autowired
private SecurityManager securityManager;
//@Autowired
private ProtocolManager protocolManager;
//@Autowired
private ActivitySessionFactory activitySessionFactory;
public void setInputDataXmlView(InputDataXmlView inputDataXmlView) {
this.inputDataXmlView = inputDataXmlView;
}
public void setActivitySessionFactory(
ActivitySessionFactory activitySessionFactory) {
this.activitySessionFactory = activitySessionFactory;
}
public void setActivityHelperLoader(
ActivityControllerHelperLoader activityControllerHelperLoader) {
this.activityControllerHelperLoader = activityControllerHelperLoader;
}
public void setProtocolManager(ProtocolManager protocolManager) {
this.protocolManager = protocolManager;
}
public void setSecurityManager(SecurityManager securityManager) {
this.securityManager = securityManager;
}
/*
@RequestMapping(value = "/activity/{activityId}", method = RequestMethod.GET)
public ModelAndView setupForm(
@PathVariable String activityId,
ModelMap model) throws IOException {
try {
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
Activity activity = protocolManager.getActivity(activityId);
if (!activity.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
ActivityControllerHelper helper = activityControllerHelperLoader
.getHelper(activity);
model.put("dataModel", helper.createDataModel());
model.put("activitySession", activitySessionFactory
.createActivitySession(user, activity));
return new ModelAndView(helper.getDataModelView(), model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show activity", ex);
}
throw ex;
}
}
@RequestMapping(value = "/activity/process", method = RequestMethod.POST)
public String processSubmit(
@ModelAttribute("activitySession") ActivitySession activitySession,
@ModelAttribute("dataModel") Object dataModel, ModelMap model,
SessionStatus session) throws IOException {
try {
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
Activity activity = activitySession.getActivity();
if (!activity.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
Properties props = activityControllerHelperLoader.getHelper(
activity).convertDataModelToActivityProperties(
activitySession.getLockedInputData(), dataModel);
for (Map.Entry<Object, Object> entry : props.entrySet()) {
activitySession.getProperties().put(entry.getKey(),
entry.getValue());
}
activitySession.executeActivity();
activitySession.finish();
model.clear();
session.setComplete();
return "redirect:/miso/activity/activities";
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to process activity", ex);
}
throw ex;
}
}
@RequestMapping(value = "/activity/input/available", method = RequestMethod.GET)
public ModelAndView ajaxAvailableInput(
@ModelAttribute("activitySession") ActivitySession activitySession)
throws IOException {
try {
if (activitySession == null) {
throw new SecurityException("Permission denied.");
}
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
Activity activity = activitySession.getActivity();
if (!activity.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
ActivityControllerHelper helper = activityControllerHelperLoader
.getHelper(activity);
Map<String, ActivityData> inputData = new HashMap<String, ActivityData>();
for (Iterator<ActivityData> iterator = activitySession
.getLockableInputData(ActivityDataFilter.FILTER_ACCEPT_ALL); iterator
.hasNext();) {
ActivityData activityData = iterator.next();
inputData.put(helper
.convertActivityDataToDisplayName(activityData),
activityData);
}
// Some kind of XML view?
return new ModelAndView(inputDataXmlView, "inputData", inputData);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to list available input", ex);
}
throw ex;
}
}
@RequestMapping(value = "/activity/input/lock", method = RequestMethod.GET)
public ModelAndView ajaxLockInput(
@ModelAttribute("activitySession") ActivitySession activitySession,
@RequestParam(value = "inputId", required = true) Long[] inputIds)
throws IOException {
try {
if (activitySession == null) {
throw new SecurityException("Permission denied.");
}
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
Activity activity = activitySession.getActivity();
if (!activity.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
// Some kind of XML view?
List<Long> ids = Arrays.asList(inputIds);
Collection<ActivityData> inputData = new HashSet<ActivityData>();
for (Iterator<ActivityData> iterator = activitySession
.getLockableInputData(ActivityDataFilter.FILTER_ACCEPT_ALL); iterator
.hasNext();) {
ActivityData lockableData = iterator.next();
if (ids.contains(lockableData.getUniqueId())) {
inputData.add(lockableData);
}
}
Collection<ActivityData> lockedData = activitySession
.lockInputData(inputData);
Map<String, ActivityData> lockedDataMap = new HashMap<String, ActivityData>();
ActivityControllerHelper helper = activityControllerHelperLoader
.getHelper(activity);
for (ActivityData activityData : lockedData) {
lockedDataMap.put(helper
.convertActivityDataToDisplayName(activityData),
activityData);
}
return new ModelAndView(inputDataXmlView, "inputData",
lockedDataMap);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to list locked data", ex);
}
throw ex;
}
}
@RequestMapping(value = "/activity/input/release", method = RequestMethod.GET)
public ModelAndView ajaxReleaseInput(
@ModelAttribute("activitySession") ActivitySession activitySession,
@RequestParam(value = "inputId", required = true) Long[] inputIds)
throws IOException {
try {
if (activitySession == null) {
throw new SecurityException("Permission denied.");
}
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
Activity activity = activitySession.getActivity();
if (!activity.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
// Some kind of XML view?
List<Long> ids = Arrays.asList(inputIds);
Collection<ActivityData> inputData = new HashSet<ActivityData>();
for (ActivityData lockedData : activitySession.getLockedInputData()) {
if (ids.contains(lockedData.getUniqueId())) {
inputData.add(lockedData);
}
}
Collection<ActivityData> releasedData = activitySession
.releaseInputData(inputData);
Map<String, ActivityData> releasedDataMap = new HashMap<String, ActivityData>();
ActivityControllerHelper helper = activityControllerHelperLoader
.getHelper(activity);
for (ActivityData activityData : releasedData) {
releasedDataMap.put(helper
.convertActivityDataToDisplayName(activityData),
activityData);
}
return new ModelAndView(inputDataXmlView, "inputData",
releasedDataMap);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to release data", ex);
}
throw ex;
}
}
*/
}