/*
* 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.ArrayList;
import java.util.Collection;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.ModelAttribute;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.SessionAttributes;
import com.eaglegenomics.simlims.core.Group;
import com.eaglegenomics.simlims.core.Protocol;
import com.eaglegenomics.simlims.core.User;
import com.eaglegenomics.simlims.core.manager.ProtocolManager;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import com.eaglegenomics.simlims.core.store.DataReferenceStore;
//import com.eaglegenomics.simlims.spring.RequestControllerHelper;
import uk.ac.bbsrc.tgac.miso.webapp.util.RequestControllerHelperLoader;
@Controller
@RequestMapping("/request")
@SessionAttributes( { "request", "dataModel" })
public class EditRequestController {
protected static final Logger log = LoggerFactory.getLogger(EditRequestController.class);
//@Autowired
private RequestControllerHelperLoader requestControllerHelperLoader;
//@Autowired
private SecurityManager securityManager;
//@Autowired
private RequestManager requestManager;
//@Autowired
private ProtocolManager protocolManager;
//@Autowired
private DataReferenceStore dataReferenceStore;
public void setRequestHelperLoader(
RequestControllerHelperLoader requestControllerHelperLoader) {
this.requestControllerHelperLoader = requestControllerHelperLoader;
}
public void setDataReferenceStore(DataReferenceStore dataReferenceStore) {
this.dataReferenceStore = dataReferenceStore;
}
public void setProtocolManager(ProtocolManager protocolManager) {
this.protocolManager = protocolManager;
}
public void setRequestManager(RequestManager requestManager) {
this.requestManager = requestManager;
}
public void setSecurityManager(SecurityManager securityManager) {
this.securityManager = securityManager;
}
@ModelAttribute("protocols")
public Collection<Protocol> populateProtocols() throws IOException {
try {
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
Collection<Protocol> protocols = new ArrayList<Protocol>();
for (Protocol protocol : protocolManager.listAllProtocols()) {
if (protocol.userCanWrite(user)) {
protocols.add(protocol);
}
}
return protocols;
} catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to list protocols", ex);
}
throw ex;
}
}
@ModelAttribute("users")
public Collection<User> populateUsers() throws IOException {
try {
return securityManager.listAllUsers();
} catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to list users", ex);
}
throw ex;
}
}
@ModelAttribute("groups")
public Collection<Group> populateGroups() throws IOException {
try {
return securityManager.listAllGroups();
} catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to list groups", ex);
}
throw ex;
}
}
/*
@RequestMapping(method = RequestMethod.GET)
public ModelAndView setupForm(
@RequestParam(value = "projectId", required = false) Long projectId,
@RequestParam(value = "requestId", required = false) Long requestId,
ModelMap model) throws IOException {
try {
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
Request request;
if (projectId != AbstractProject.UNSAVED_ID) {
request = requestManager.getProjectById(projectId)
.createRequest(user);
} else {
request = requestManager.getRequestById(requestId);
}
if (!request.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
model.put("request", request);
model.put("dataModel", "");
return new ModelAndView("/pages/editRequest.jsp", model);
} catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show request", ex);
}
throw ex;
}
}
@RequestMapping(method = RequestMethod.POST)
public ModelAndView processSubmit(
@ModelAttribute("request") Request request,
@ModelAttribute("dataModel") Object dataModel, ModelMap model,
SessionStatus session) throws IOException {
try {
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
String view = "redirect:/miso/projects";
if (!request.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
if (request.getRequestId() == Request.UNSAVED_ID) {
RequestControllerHelper helper = requestControllerHelperLoader
.getHelper(protocolManager.getProtocol(request
.getProtocolUniqueIdentifier()));
if ("".equals(dataModel)) {
model.put("dataModel", helper.createDataModel());
view = helper.getDataModelView();
} else {
requestManager.saveRequest(request);
queueData(request, helper
.convertDataModelToInputData(dataModel));
session.setComplete();
model.clear();
}
} else {
// Save the request.
requestManager.saveRequest(request);
session.setComplete();
model.clear();
}
return new ModelAndView(view, model);
} catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to save request", ex);
}
throw ex;
}
}
private void queueData(Request request, Collection<?> data)
throws IOException {
Collection<ActivityData> inputData = new HashSet<ActivityData>();
Protocol protocol = protocolManager.getProtocol(request
.getProtocolUniqueIdentifier());
String startpoint = protocol.getStartpoint();
for (Object obj : data) {
DataReference ref = dataReferenceStore.create(obj);
ref.save();
ActivityData act = new BasicActivityData();
act.setActivityAlias(startpoint);
act.setDataReference(ref);
act.setActivity(protocol.getActivityAliasMap().get(startpoint));
Entry entry = act.createEntry();
entry.setRequest(request);
entry.setExecutionCount(request.getExecutionCount());
entry.setProtocol(protocolManager.getProtocol(request
.getProtocolUniqueIdentifier()));
act.getIndexedEntries().put(ActivityData.NO_INDEX, entry);
inputData.add(act);
}
protocolManager.setupInputData(request.getSecurityProfile().getOwner(),
inputData);
}
*/
}