/*
* 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.springframework.jdbc.core.JdbcTemplate;
import uk.ac.bbsrc.tgac.miso.core.data.Project;
import com.eaglegenomics.simlims.core.User;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.security.core.context.SecurityContextHolder;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import org.springframework.beans.factory.annotation.Autowired;
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.illumina.IlluminaRun;
import uk.ac.bbsrc.tgac.miso.core.data.impl.ls454.LS454Run;
import uk.ac.bbsrc.tgac.miso.core.data.impl.solid.SolidRun;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedRunException;
import uk.ac.bbsrc.tgac.miso.core.exception.SubmissionException;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.manager.SubmissionManager;
import uk.ac.bbsrc.tgac.miso.core.manager.FilesManager;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import uk.ac.bbsrc.tgac.miso.sqlstore.util.DbUtils;
import java.io.IOException;
import java.util.*;
@Controller
@RequestMapping("/submission")
@SessionAttributes("submission")
public class EditSubmissionController {
protected static final Logger log = LoggerFactory.getLogger(EditSubmissionController.class);
@Autowired
private SecurityManager securityManager;
@Autowired
private RequestManager requestManager;
@Autowired
private DataObjectFactory dataObjectFactory;
@Autowired
private FilesManager misoFileManager;
@Autowired
private SubmissionManager submissionManager;
@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 void setMisoFileManager(FilesManager misoFileManager) {
this.misoFileManager = misoFileManager;
}
public void setSubmissionManager(SubmissionManager submissionManager) {
this.submissionManager = submissionManager;
}
@ModelAttribute("maxLengths")
public Map<String, Integer> maxLengths() throws IOException {
return DbUtils.getColumnSizes(interfaceTemplate, "Submission");
}
@ModelAttribute("projects")
public Collection<Project> populateProjects() throws IOException {
//User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
List<Project> projects = new ArrayList<Project>(requestManager.listAllProjects());
/*
for (Project p : projects) {
Collection<Run> runs = requestManager.listAllRunsByProjectId(p.getProjectId());
for (Run r : runs) {
if (r instanceof IlluminaRun) {
IlluminaRun ir = (IlluminaRun)r;
ir.setFlowcells(requestManager.listLaneFlowcellsByRunId(ir.getRunId()));
}
else if (r instanceof SolidRun) {
SolidRun sr = (SolidRun)r;
sr.setFlowcells(requestManager.listChamberFlowcellsByRunId(sr.getRunId()));
}
else if (r instanceof LS454Run) {
LS454Run lr = (LS454Run)r;
lr.setFlowcells(requestManager.listChamberFlowcellsByRunId(lr.getRunId()));
}
}
*/
/*
Collection<Study> studies = requestManager.listAllStudiesByProjectId(p.getProjectId());
p.setStudies(studies);
for (Study s : studies) {
Collection<Experiment> experiments = requestManager.listAllExperimentsByStudyId(s.getStudyId());
s.setExperiments(experiments);
}
*/
//}
Collections.sort(projects);
return projects;
}
@ModelAttribute("studies")
public Collection<Study> populateStudies() throws IOException {
//User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
return requestManager.listAllStudies();
}
@ModelAttribute("samples")
public Collection<Sample> populateSamples() throws IOException {
//User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
return requestManager.listAllSamples();
}
@ModelAttribute("runs")
public Collection<Run> populateRuns() throws IOException {
//User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
return requestManager.listAllRuns();
}
@ModelAttribute("experiments")
public Collection<Experiment> populateExperiments() throws IOException {
//User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
return requestManager.listAllExperiments();
}
@ModelAttribute("availableElements")
public Collection<Submittable> populateElements() throws IOException {
ArrayList<Submittable> list = new ArrayList<Submittable>();
list.addAll(populateSamples());
list.addAll(populateStudies());
list.addAll(populateExperiments());
return list;
}
@RequestMapping(value = "/new", method = RequestMethod.GET)
public ModelAndView newSubmission(ModelMap model) throws IOException {
return setupForm(Submission.UNSAVED_ID, model);
}
@RequestMapping(value = "/{submissionId}", method = RequestMethod.GET)
public ModelAndView setupForm(@PathVariable Long submissionId,
ModelMap model) throws IOException {
try {
Submission submission = null;
if (submissionId == Submission.UNSAVED_ID) {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
submission = dataObjectFactory.getSubmission(user);
model.put("title", "New Submission");
}
else {
submission = requestManager.getSubmissionById(submissionId);
model.put("title", "Submission "+submissionId);
model.put("prettyMetadata", submissionManager.prettifySubmissionMetadata(submission));
}
if (submission == null) {
throw new SecurityException("No such Submission");
}
model.put("formObj", submission);
model.put("submission", submission);
return new ModelAndView("/pages/editSubmission.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show submission", ex);
}
throw ex;
}
catch (SubmissionException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to show submission", e);
}
throw new IOException(e);
}
}
@RequestMapping(method = RequestMethod.POST)
public String processSubmit(@ModelAttribute("submission") Submission submission,
ModelMap model, SessionStatus session) throws IOException, MalformedRunException {
try {
requestManager.saveSubmission(submission);
session.setComplete();
model.clear();
return "redirect:/miso/submission/"+submission.getId();
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to save submission", ex);
}
throw ex;
}
}
}