/*
* 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.Arrays;
import java.util.Collection;
import java.util.Map;
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 uk.ac.bbsrc.tgac.miso.core.data.Project;
import com.eaglegenomics.simlims.core.User;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import uk.ac.bbsrc.tgac.miso.core.data.AbstractStudy;
import uk.ac.bbsrc.tgac.miso.core.data.Study;
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 uk.ac.bbsrc.tgac.miso.core.util.LimsUtils;
import uk.ac.bbsrc.tgac.miso.sqlstore.util.DbUtils;
@Controller
@RequestMapping("/study")
@SessionAttributes("study")
public class EditStudyController {
protected static final Logger log = LoggerFactory.getLogger(EditStudyController.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;
}
public Project populateProject(@PathVariable Long projectId) throws IOException {
try {
return requestManager.getProjectById(projectId);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to get parent project", ex);
}
throw ex;
}
}
@ModelAttribute("maxLengths")
public Map<String, Integer> maxLengths() throws IOException {
return DbUtils.getColumnSizes(interfaceTemplate, "Study");
}
@ModelAttribute("studyTypes")
public Collection<String> populateStudyTypes() throws IOException {
return requestManager.listAllStudyTypes();
}
@RequestMapping(value = "/new/{projectId}", method = RequestMethod.GET)
public ModelAndView newAssignedProject(@PathVariable Long projectId,
ModelMap model) throws IOException {
return setupForm(AbstractStudy.UNSAVED_ID, projectId, model);
}
@RequestMapping(value = "/rest/{studyId}", method = RequestMethod.GET)
public @ResponseBody Study jsonRest(@PathVariable Long studyId) throws IOException {
return requestManager.getStudyById(studyId);
}
@RequestMapping(value = "/{studyId}", method = RequestMethod.GET)
public ModelAndView setupForm(@PathVariable Long studyId,
ModelMap model) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Study study = requestManager.getStudyById(studyId);
Project project;
if (study != null) {
if (!study.userCanRead(user)) {
throw new SecurityException("Permission denied.");
}
project = study.getProject();
model.put("formObj", study);
model.put("project", project);
model.put("study", study);
model.put("title", "Study "+studyId);
}
else {
throw new SecurityException("No such Study");
}
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, study, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, study, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, study, securityManager.listAllGroups()));
return new ModelAndView("/pages/editStudy.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show Study", ex);
}
throw ex;
}
}
@RequestMapping(value = "/{studyId}/project/{projectId}", method = RequestMethod.GET)
public ModelAndView setupForm(@PathVariable Long studyId,
@PathVariable Long projectId,
ModelMap model) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Study study = null;
if (studyId == AbstractStudy.UNSAVED_ID) {
study = dataObjectFactory.getStudy(user);
model.put("title", "New Study");
}
else {
study = requestManager.getStudyById(studyId);
model.put("title", "Study "+studyId);
}
Project project = requestManager.getProjectById(projectId);
model.addAttribute("project", project);
study.setProject(project);
if (Arrays.asList(user.getRoles()).contains("ROLE_TECH")) {
SecurityProfile sp = new SecurityProfile(user);
LimsUtils.inheritUsersAndGroups(study, project.getSecurityProfile());
sp.setOwner(user);
study.setSecurityProfile(sp);
} else {
study.inheritPermissions(project);
}
if (!study.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
model.put("formObj", study);
model.put("study", study);
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, study, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, study, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, study, securityManager.listAllGroups()));
return new ModelAndView("/pages/editStudy.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show Study", ex);
}
throw ex;
}
}
@RequestMapping(method = RequestMethod.POST)
public String processSubmit(@ModelAttribute("study") Study study,
ModelMap model,
SessionStatus session) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
if (!study.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
requestManager.saveStudy(study);
session.setComplete();
model.clear();
return "redirect:/miso/study/"+study.getId();
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to save Study", ex);
}
throw ex;
}
}
}