/*
* 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.text.SimpleDateFormat;
import java.util.*;
import net.sf.json.JSONArray;
import net.sf.json.JSONObject;
import net.sourceforge.fluxion.ajax.util.JSONUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.propertyeditors.CustomDateEditor;
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.WebDataBinder;
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 com.eaglegenomics.simlims.core.User;
import uk.ac.bbsrc.tgac.miso.core.data.impl.*;
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.data.type.PlatformType;
import uk.ac.bbsrc.tgac.miso.core.data.type.QcType;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedLibraryQcException;
import uk.ac.bbsrc.tgac.miso.core.manager.IssueTrackerManager;
import uk.ac.bbsrc.tgac.miso.core.util.AliasComparator;
import uk.ac.bbsrc.tgac.miso.core.util.LimsUtils;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import uk.ac.bbsrc.tgac.miso.core.manager.FilesManager;
import uk.ac.bbsrc.tgac.miso.core.security.util.LimsSecurityUtils;
import uk.ac.bbsrc.tgac.miso.sqlstore.util.DbUtils;
@Controller
@RequestMapping("/project")
@SessionAttributes("project")
public class EditProjectController {
protected static final Logger log = LoggerFactory.getLogger(EditProjectController.class);
@Autowired
private SecurityManager securityManager;
@Autowired
private RequestManager requestManager;
@Autowired
private FilesManager filesManager;
@Autowired
private DataObjectFactory dataObjectFactory;
public void setDataObjectFactory(DataObjectFactory dataObjectFactory) {
this.dataObjectFactory = dataObjectFactory;
}
public void setSecurityManager(SecurityManager securityManager) {
this.securityManager = securityManager;
}
public void setRequestManager(RequestManager requestManager) {
this.requestManager = requestManager;
}
public void setFilesManager(FilesManager filesManager) {
this.filesManager = filesManager;
}
@Autowired
private JdbcTemplate interfaceTemplate;
public void setInterfaceTemplate(JdbcTemplate interfaceTemplate) {
this.interfaceTemplate = interfaceTemplate;
}
@InitBinder
public void initBinder(WebDataBinder binder) {
CustomDateEditor cde = new CustomDateEditor(new SimpleDateFormat("dd/MM/yyyy"), true);
binder.registerCustomEditor(Date.class, cde);
}
public Map<Integer, String> populateProjectFiles(Long projectId) throws IOException {
if (projectId != AbstractProject.UNSAVED_ID) {
Project p = requestManager.getProjectById(projectId);
if (p != null) {
//User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Map<Integer, String> fileMap = new HashMap<Integer, String>();
for (String s : filesManager.getFileNames(Project.class, projectId.toString())) {
fileMap.put(s.hashCode(), s);
}
return fileMap;
}
}
return Collections.emptyMap();
}
@ModelAttribute("maxLengths")
public Map<String, Integer> maxLengths() throws IOException {
return DbUtils.getColumnSizes(interfaceTemplate, "Project");
}
@ModelAttribute("sampleQcTypesString")
public String sampleTypesString() throws IOException {
List<String> types = new ArrayList<String>();
for (QcType s : requestManager.listAllSampleQcTypes()) {
types.add("\"" + s.getQcTypeId() + "\"" + ":" + "\"" + s.getName() + "\"");
}
Collections.sort(types);
return LimsUtils.join(types, ",");
}
@ModelAttribute("sampleQCUnits")
public String sampleQCUnits() throws IOException {
return AbstractSampleQC.UNITS;
}
@ModelAttribute("libraryQcTypesString")
public String libraryTypesString() throws IOException {
List<String> types = new ArrayList<String>();
List<QcType> libraryQcTypes = new ArrayList<QcType>(requestManager.listAllLibraryQcTypes());
Collections.sort(libraryQcTypes);
for (QcType s : libraryQcTypes) {
types.add("\"" + s.getQcTypeId() + "\"" + ":" + "\"" + s.getName() + "\"");
}
return LimsUtils.join(types, ",");
}
public Collection<Run> populateProjectRuns(long projectId) throws IOException {
List<Run> runs = new ArrayList<Run>(requestManager.listAllRunsByProjectId(projectId));
try {
Collections.sort(runs, new AliasComparator(Run.class));
for (Run r : runs) {
RunImpl ri = (RunImpl) r;
ri.setSequencerPartitionContainers(new ArrayList<SequencerPartitionContainer<SequencerPoolPartition>>(
requestManager.listSequencerPartitionContainersByRunId(r.getId())));
}
return runs;
}
catch (NoSuchMethodException e) {
throw new IOException(e);
}
}
public Collection<Library> populateProjectLibraries(long projectId) throws IOException {
List<Library> libraries = new ArrayList<Library>(requestManager.listAllLibrariesByProjectId(projectId));
try {
Collections.sort(libraries, new AliasComparator(Library.class));
for (Library l : libraries) {
for (LibraryQC qc : requestManager.listAllLibraryQCsByLibraryId(l.getId())) {
try {
l.addQc(qc);
}
catch (MalformedLibraryQcException e) {
throw new IOException(e);
}
}
}
}
catch (NoSuchMethodException e) {
throw new IOException(e);
}
return libraries;
}
public Collection<LibraryDilution> populateProjectLibraryDilutions(Collection<Library> projectLibraries) throws IOException {
List<LibraryDilution> dilutions = new ArrayList<LibraryDilution>();
for (Library l : projectLibraries) {
dilutions.addAll(requestManager.listAllLibraryDilutionsByLibraryId(l.getId()));
}
Collections.sort(dilutions);
return dilutions;
}
public Collection<LibraryDilution> populateProjectLibraryDilutions(long projectId) throws IOException {
List<LibraryDilution> dilutions = new ArrayList<LibraryDilution>(requestManager.listAllLibraryDilutionsByProjectId(projectId));
Collections.sort(dilutions);
return dilutions;
}
public Collection<Pool> populateProjectPools(long projectId) throws IOException {
List<Pool> pools = new ArrayList<Pool>(requestManager.listPoolsByProjectId(projectId));
Collections.sort(pools);
return pools;
}
public boolean existsAnyEmPcrLibrary(Collection<LibraryDilution> projectLibraryDilutions) throws IOException {
boolean exists = false;
for (LibraryDilution dil : projectLibraryDilutions) {
if (!dil.getLibrary().getPlatformName().equals(PlatformType.ILLUMINA.getKey())) {
exists = true;
}
}
return exists;
}
public boolean existsAnyEmPcrLibrary(long projectId) throws IOException {
boolean exists = false;
for (LibraryDilution dil : populateProjectLibraryDilutions(projectId)) {
if (!dil.getLibrary().getPlatformName().equals(PlatformType.ILLUMINA.getKey())) {
exists = true;
}
}
return exists;
}
public Collection<emPCR> populateProjectEmPCRs(long projectId) throws IOException {
List<emPCR> pcrs = new ArrayList<emPCR>(requestManager.listAllEmPCRsByProjectId(projectId));
Collections.sort(pcrs);
return pcrs;
}
public Collection<emPCRDilution> populateProjectEmPcrDilutions(Collection<emPCR> projectEmPCRs) throws IOException {
List<emPCRDilution> dilutions = new ArrayList<emPCRDilution>();
for (emPCR e : projectEmPCRs) {
dilutions.addAll(requestManager.listAllEmPcrDilutionsByEmPcrId(e.getId()));
}
Collections.sort(dilutions);
return dilutions;
}
public Collection<emPCRDilution> populateProjectEmPcrDilutions(long projectId) throws IOException {
List<emPCRDilution> dilutions = new ArrayList<emPCRDilution>(requestManager.listAllEmPcrDilutionsByProjectId(projectId));
Collections.sort(dilutions);
return dilutions;
}
public Collection<Plate<? extends List<? extends Plateable>, ? extends Plateable>> populateProjectPlates(long projectId) throws IOException {
List<Plate<? extends List<? extends Plateable>, ? extends Plateable>> plates = new ArrayList<Plate<? extends List<? extends Plateable>, ? extends Plateable>>(requestManager.listAllPlatesByProjectId(projectId));
Collections.sort(plates);
return plates;
}
@RequestMapping(value = "/graph/{projectId}", method = RequestMethod.GET)
public
@ResponseBody
JSONObject graphRest(@PathVariable Long projectId) throws IOException {
JSONObject j = new JSONObject();
try {
Collection<Sample> samples = requestManager.listAllSamplesByProjectId(projectId);
Collection<Run> runs = requestManager.listAllRunsByProjectId(projectId);
Collection<Study> studies = requestManager.listAllStudiesByProjectId(projectId);
JSONObject runsJSON = new JSONObject();
JSONObject studiesJSON = new JSONObject();
JSONObject samplesJSON = new JSONObject();
for (Run run : runs) {
if (run.getStatus() != null
&& run.getStatus().getHealth() != null
&& run.getStatus().getHealth().getKey().equals("Completed")) {
runsJSON.put(run.getName(), "1");
}
else {
runsJSON.put(run.getName(), "0");
}
}
for (Study study : studies) {
Collection<Experiment> experiments = requestManager.listAllExperimentsByStudyId(study.getId());
if (experiments.size() == 0) {
studiesJSON.put(study.getName(), "2");
}
else {
JSONObject experimentsJSON = new JSONObject();
for (Experiment e : experiments) {
experimentsJSON.put(e.getName(), "2");
}
studiesJSON.put(study.getName(), experimentsJSON);
}
}
for (Sample sample : samples) {
Collection<Library> libraries = requestManager.listAllLibrariesBySampleId(sample.getId());
if (libraries.size() == 0) {
if (sample.getQcPassed()) {
samplesJSON.put(sample.getName(), "1");
}
else {
samplesJSON.put(sample.getName(), "0");
}
}
else {
JSONObject librariesJSON = new JSONObject();
for (Library library : libraries) {
Collection<LibraryDilution> lds = requestManager.listAllLibraryDilutionsByLibraryId(library.getId());
if (lds.size() > 0) {
JSONObject dilutionsJSON = new JSONObject();
for (LibraryDilution ld : lds) {
dilutionsJSON.put(ld.getName(), "2");
}
librariesJSON.put(library.getName(), dilutionsJSON);
}
else {
if (library.getLibraryQCs().size() > 0) {
librariesJSON.put(library.getName(), "1");
}
else {
librariesJSON.put(library.getName(), "0");
}
}
}
samplesJSON.put(sample.getName(), librariesJSON);
}
}
j.put("Runs", runsJSON);
j.put("Studies", studiesJSON);
j.put("Samples", samplesJSON);
return j;
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
@RequestMapping(value = "/new", method = RequestMethod.GET)
public ModelAndView setupForm(ModelMap model) throws IOException {
return setupForm(AbstractProject.UNSAVED_ID, model);
}
@RequestMapping(value = "/{projectId}", method = RequestMethod.GET)
public ModelAndView setupForm(@PathVariable Long projectId,
ModelMap model) throws IOException {
try {
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
Project project = null;
if (projectId == AbstractProject.UNSAVED_ID) {
project = dataObjectFactory.getProject(user);
model.put("title", "New Project");
}
else {
project = requestManager.getProjectById(projectId);
model.put("title", "Project " + projectId);
model.put("projectRuns", populateProjectRuns(projectId));
Collection<Library> libraries = populateProjectLibraries(projectId);
model.put("projectLibraries", libraries);
Collection<LibraryDilution> libraryDilutions = populateProjectLibraryDilutions(libraries);
model.put("projectLibraryDilutions", libraryDilutions);
model.put("existsAnyEmPcrLibrary", existsAnyEmPcrLibrary(libraryDilutions));
Collection<emPCR> emPcrs = populateProjectEmPCRs(projectId);
model.put("projectEmPcrs", emPcrs);
model.put("projectEmPcrDilutions", populateProjectEmPcrDilutions(emPcrs));
model.put("projectPools", populateProjectPools(projectId));
model.put("projectPlates", populateProjectPlates(projectId));
}
if (project == null) {
throw new SecurityException("No such Project");
}
if (!project.userCanRead(user)) {
throw new SecurityException("Permission denied.");
}
model.put("formObj", project);
model.put("project", project);
model.put("projectFiles", populateProjectFiles(projectId));
//model.put("projectRuns", requestManager.listAllRunsByProjectId(projectId));
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, project, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, project, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, project, securityManager.listAllGroups()));
model.put("overviews", project.getOverviews());
Map<Long, String> overviewMap = new HashMap<Long, String>();
for (ProjectOverview po : project.getOverviews()) {
//log.debug(po.getWatchers().toString());
if (po.getWatchers().contains(user)) {
overviewMap.put(po.getOverviewId(), user.getLoginName());
}
}
model.put("overviewMap", overviewMap);
return new ModelAndView("/pages/editProject.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show project", ex);
}
throw ex;
}
}
@RequestMapping(method = RequestMethod.POST)
public String processSubmit(@ModelAttribute("project") Project project,
ModelMap model, SessionStatus session) throws IOException {
try {
User user = securityManager
.getUserByLoginName(SecurityContextHolder.getContext()
.getAuthentication().getName());
if (!project.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
requestManager.saveProject(project);
session.setComplete();
model.clear();
return "redirect:/miso/project/" + project.getProjectId();
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to save project", ex);
}
throw ex;
}
}
}