/*
* 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 com.eaglegenomics.simlims.core.SecurityProfile;
import com.eaglegenomics.simlims.core.User;
import org.springframework.jdbc.core.JdbcTemplate;
import uk.ac.bbsrc.tgac.miso.core.data.type.LibrarySelectionType;
import uk.ac.bbsrc.tgac.miso.core.data.type.LibraryStrategyType;
import uk.ac.bbsrc.tgac.miso.core.data.type.LibraryType;
import uk.ac.bbsrc.tgac.miso.core.data.type.PlatformType;
import uk.ac.bbsrc.tgac.miso.core.service.tagbarcode.TagBarcodeStrategy;
import uk.ac.bbsrc.tgac.miso.core.service.tagbarcode.TagBarcodeStrategyResolverService;
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.manager.RequestManager;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
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.*;
import uk.ac.bbsrc.tgac.miso.core.data.impl.LibraryDilution;
import uk.ac.bbsrc.tgac.miso.core.data.impl.emPCR;
import uk.ac.bbsrc.tgac.miso.core.data.impl.emPCRDilution;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedLibraryException;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.security.util.LimsSecurityUtils;
import uk.ac.bbsrc.tgac.miso.sqlstore.util.DbUtils;
import uk.ac.bbsrc.tgac.miso.webapp.context.ApplicationContextProvider;
import uk.ac.bbsrc.tgac.miso.webapp.util.MisoPropertyExporter;
import java.io.IOException;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* uk.ac.bbsrc.tgac.miso.webapp.controller
* <p/>
* Info
*
* @author Rob Davey
* @since 0.0.2
*/
@Controller
@RequestMapping("/library")
@SessionAttributes("library")
public class EditLibraryController {
protected static final Logger log = LoggerFactory.getLogger(EditLibraryController.class);
@Autowired
private SecurityManager securityManager;
@Autowired
private RequestManager requestManager;
@Autowired
private DataObjectFactory dataObjectFactory;
@Autowired
private JdbcTemplate interfaceTemplate;
@Autowired
private TagBarcodeStrategyResolverService tagBarcodeStrategyResolverService;
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 setTagBarcodeStrategyResolverService(TagBarcodeStrategyResolverService tagBarcodeStrategyResolverService) {
this.tagBarcodeStrategyResolverService = tagBarcodeStrategyResolverService;
}
@Autowired
private ApplicationContextProvider applicationContextProvider;
public void setApplicationContextProvider(ApplicationContextProvider applicationContextProvider) {
this.applicationContextProvider = applicationContextProvider;
}
@ModelAttribute("metrixEnabled")
public Boolean isMetrixEnabled() {
MisoPropertyExporter exporter = (MisoPropertyExporter)applicationContextProvider.getApplicationContext().getBean("propertyConfigurer");
Map<String, String> misoProperties = exporter.getResolvedProperties();
return misoProperties.containsKey("miso.notification.interop.enabled") && Boolean.parseBoolean(misoProperties.get("miso.notification.interop.enabled"));
}
public Map<String, Library> getAdjacentLibrariesInProject(Library l, Project p) throws IOException {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Library prevL = null;
Library nextL = null;
if (p != null) {
long projectId = p.getId();
if (p.getId() == projectId) {
List<Sample> samples = new ArrayList<>(requestManager.listAllSamplesByProjectId(projectId));
Collections.sort(samples);
List<Library> allLibs = new ArrayList<>();
Map<String, Library> ret = new HashMap<>();
for (Sample s : samples) {
List<Library> samLibs = new ArrayList<>(requestManager.listAllLibrariesBySampleId(s.getId()));
if (!samLibs.isEmpty()) {
Collections.sort(samLibs);
allLibs.addAll(samLibs);
}
}
for (int i = 0; i < allLibs.size(); i++) {
if (allLibs.get(i).equals(l)) {
if (i != 0 && allLibs.get(i-1) != null) {
prevL = allLibs.get(i-1);
}
if (i != allLibs.size()-1 && allLibs.get(i+1) != null) {
nextL = allLibs.get(i+1);
}
break;
}
}
ret.put("previousLibrary", prevL);
ret.put("nextLibrary", nextL);
return ret;
}
}
return Collections.emptyMap();
}
public List<Pool<? extends Poolable>> getPoolsByLibrary(Library l) throws IOException {
if (!l.getLibraryDilutions().isEmpty()) {
List<Pool<? extends Poolable>> pools = new ArrayList<>(requestManager.listPoolsByLibraryId(l.getId()));
Collections.sort(pools);
return pools;
}
return Collections.emptyList();
}
public Set<Run> getRunsByLibraryPools(List<Pool<? extends Poolable>> pools) throws IOException {
Set<Run> runs = new TreeSet<>();
for (Pool<? extends Poolable> pool : pools) {
Collection<Run> prs = requestManager.listRunsByPoolId(pool.getId());
runs.addAll(prs);
}
return runs;
}
public Collection<LibraryType> populateLibraryTypesByPlatform(String platform) throws IOException {
List<LibraryType> types = new ArrayList<LibraryType>(requestManager.listLibraryTypesByPlatform(platform));
Collections.sort(types);
return types;
}
public Collection<LibraryType> populateLibraryTypes() throws IOException {
List<LibraryType> types = new ArrayList<LibraryType>(requestManager.listAllLibraryTypes());
Collections.sort(types);
return types;
}
@ModelAttribute("maxLengths")
public Map<String, Integer> maxLengths() throws IOException {
return DbUtils.getColumnSizes(interfaceTemplate, "Library");
}
@ModelAttribute("platformNames")
public Collection<String> populatePlatformNames() throws IOException {
List<String> types = new ArrayList<String>(requestManager.listDistinctPlatformNames());
Collections.sort(types);
return types;
}
@ModelAttribute("platformNamesString")
public String platformNamesString() throws IOException {
List<String> names = new ArrayList<String>();
List<String> pn = new ArrayList<String>(populatePlatformNames());
for (String name : pn) {
names.add("\"" + name + "\"" + ":" + "\"" + name + "\"");
}
if (!pn.isEmpty()) {
names.add("\"selected\":"+"\"" + pn.get(0) + "\"");
}
return LimsUtils.join(names, ",");
}
@ModelAttribute("libraryTypesString")
public String libraryTypesString() throws IOException {
List<String> types = new ArrayList<String>();
for (LibraryType t : populateLibraryTypes()) {
types.add("\"" + t.getDescription() + "\"" + ":" + "\"" + t.getDescription() + "\"");
}
return LimsUtils.join(types, ",");
}
@ModelAttribute("librarySelectionTypes")
public Collection<LibrarySelectionType> populateLibrarySelectionTypes() throws IOException {
List<LibrarySelectionType> types = new ArrayList<LibrarySelectionType>(requestManager.listAllLibrarySelectionTypes());
Collections.sort(types);
return types;
}
@ModelAttribute("librarySelectionTypesString")
public String librarySelectionTypesString() throws IOException {
List<String> types = new ArrayList<String>();
for (LibrarySelectionType t : populateLibrarySelectionTypes()) {
types.add("\"" + t.getName() + "\"" + ":" + "\"" + t.getName() + "\"");
}
return LimsUtils.join(types, ",");
}
@ModelAttribute("libraryStrategyTypes")
public Collection<LibraryStrategyType> populateLibraryStrategyTypes() throws IOException {
List<LibraryStrategyType> types = new ArrayList<LibraryStrategyType>(requestManager.listAllLibraryStrategyTypes());
Collections.sort(types);
return types;
}
@ModelAttribute("libraryStrategyTypesString")
public String libraryStrategyTypesString() throws IOException {
List<String> types = new ArrayList<String>();
for (LibraryStrategyType t : populateLibraryStrategyTypes()) {
types.add("\"" + t.getName() + "\"" + ":" + "\"" + t.getName() + "\"");
}
return LimsUtils.join(types, ",");
}
public Collection<TagBarcodeStrategy> populateAvailableTagBarcodeStrategies(Library l) throws IOException {
List<TagBarcodeStrategy> strategies = new ArrayList<TagBarcodeStrategy>(tagBarcodeStrategyResolverService.getTagBarcodeStrategiesByPlatform(PlatformType.get(l.getPlatformName())));
return strategies;
}
public Collection<TagBarcode> populateAvailableTagBarcodes(Library l) throws IOException {
List<TagBarcode> barcodes = new ArrayList<TagBarcode>(requestManager.listAllTagBarcodesByPlatform(l.getPlatformName()));
Collections.sort(barcodes);
return barcodes;
}
public String tagBarcodesString(String platformName) throws IOException {
List<TagBarcode> tagBarcodes = new ArrayList<TagBarcode>(requestManager.listAllTagBarcodesByPlatform(platformName));
Collections.sort(tagBarcodes);
List<String> names = new ArrayList<String>();
for (TagBarcode tb : tagBarcodes) {
names.add("\"" + tb.getName() + " ("+tb.getSequence()+")\"" + ":" + "\"" + tb.getId() + "\"");
}
return LimsUtils.join(names, ",");
}
@ModelAttribute("libraryInitialConcentrationUnits")
public String libraryInitialConcentrationUnits() {
return AbstractLibrary.UNITS;
}
@ModelAttribute("libraryQCUnits")
public String libraryQCUnits() {
return AbstractLibraryQC.UNITS;
}
@ModelAttribute("libraryDilutionUnits")
public String libraryDilutionUnits() {
return LibraryDilution.UNITS;
}
@ModelAttribute("emPCRUnits")
public String emPCRUnits() {
return emPCR.UNITS;
}
@ModelAttribute("emPCRDilutionUnits")
public String emPCRDilutionUnits() {
return emPCRDilution.UNITS;
}
@RequestMapping(value = "librarytypes", method = RequestMethod.GET)
public @ResponseBody String jsonRestLibraryTypes(@RequestParam("platform") String platform) throws IOException {
if (platform != null && !"".equals(platform)) {
List<String> types = new ArrayList<String>();
for (LibraryType t : populateLibraryTypesByPlatform(platform)) {
types.add("\"" + t.getDescription() + "\"" + ":" + "\"" + t.getDescription() + "\"");
}
return "{"+ LimsUtils.join(types, ",")+"}";
}
else {
return "{}";
}
}
@RequestMapping(value = "barcodeStrategies", method = RequestMethod.GET)
public @ResponseBody String jsonRestBarcodeStrategies(@RequestParam("platform") String platform) throws IOException {
if (platform != null && !"".equals(platform)) {
List<String> types = new ArrayList<String>();
for (TagBarcodeStrategy t : tagBarcodeStrategyResolverService.getTagBarcodeStrategiesByPlatform(PlatformType.get(platform))) {
types.add("\"" + t.getName() + "\"" + ":" + "\"" + t.getName() + "\"");
}
return "{"+ LimsUtils.join(types, ",")+"}";
}
else {
return "{}";
}
}
@RequestMapping(value = "barcodesForPosition", method = RequestMethod.GET)
public @ResponseBody String jsonRestTagBarcodes(@RequestParam("barcodeStrategy") String barcodeStrategy, @RequestParam("position") String position) throws IOException {
if (barcodeStrategy != null && !"".equals(barcodeStrategy)) {
TagBarcodeStrategy tbs = tagBarcodeStrategyResolverService.getTagBarcodeStrategy(barcodeStrategy);
if (tbs != null) {
List<TagBarcode> tagBarcodes = new ArrayList<TagBarcode>(tbs.getApplicableBarcodesForPosition(Integer.parseInt(position)));
List<String> names = new ArrayList<String>();
for (TagBarcode tb : tagBarcodes) {
names.add("\"" + tb.getId() + "\"" + ":" + "\"" + tb.getName() + " ("+tb.getSequence()+")\"");
}
return "{"+LimsUtils.join(names, ",")+"}";
}
else {
return "{}";
}
}
else {
return "{}";
}
}
public Collection<emPCR> populateEmPcrs(User user, Library library) throws IOException {
Collection<emPCR> pcrs = new HashSet<emPCR>();
for (emPCR pcr : requestManager.listAllEmPCRs()) {
for (LibraryDilution ldil : library.getLibraryDilutions()) {
if (pcr.getLibraryDilution().getId() == ldil.getId()) {
pcrs.add(pcr);
}
}
}
return pcrs;
}
public Collection<emPCRDilution> populateEmPcrDilutions(User user, Collection<emPCR> pcrs) throws IOException {
Collection<emPCRDilution> dilutions = new HashSet<emPCRDilution>();
for (emPCR pcr : pcrs) {
for (emPCRDilution dilution : requestManager.listAllEmPcrDilutionsByEmPcrId(pcr.getId())) {
dilution.setEmPCR(pcr);
dilutions.add(dilution);
}
}
return dilutions;
}
@RequestMapping(value = "/new/{sampleId}", method = RequestMethod.GET)
public ModelAndView newAssignedLibrary(@PathVariable Long sampleId,
ModelMap model) throws IOException {
return setupForm(AbstractLibrary.UNSAVED_ID, sampleId, model);
}
@RequestMapping(value = "/{libraryId}", method = RequestMethod.GET)
public ModelAndView setupForm(@PathVariable Long libraryId,
ModelMap model) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Library library = requestManager.getLibraryById(libraryId);
if (library == null) {
throw new SecurityException("No such Library.");
}
if (!library.userCanRead(user)) {
throw new SecurityException("Permission denied.");
}
model.put("formObj", library);
model.put("library", library);
Collection<emPCR> pcrs = populateEmPcrs(user, library);
model.put("emPCRs", pcrs);
model.put("emPcrDilutions", populateEmPcrDilutions(user, pcrs));
if (library.getTagBarcodes() != null && !library.getTagBarcodes().isEmpty() && library.getTagBarcodes().get(1) != null) {
model.put("selectedTagBarcodeStrategy", library.getTagBarcodes().get(1).getStrategyName());
model.put("availableTagBarcodeStrategyBarcodes", tagBarcodeStrategyResolverService.getTagBarcodeStrategy(library.getTagBarcodes().get(1).getStrategyName()).getApplicableBarcodes());
}
model.put("availableTagBarcodeStrategies", populateAvailableTagBarcodeStrategies(library));
Map<String, Library> adjacentLibraries = getAdjacentLibrariesInProject(library, library.getSample().getProject());
if (!adjacentLibraries.isEmpty()) {
model.put("previousLibrary", adjacentLibraries.get("previousLibrary"));
model.put("nextLibrary", adjacentLibraries.get("nextLibrary"));
}
List<Pool<? extends Poolable>> pools = getPoolsByLibrary(library);
Map<Long, Library> poolLibraryMap = new HashMap<>();
for (Pool pool : pools) {
poolLibraryMap.put(pool.getId(), library);
}
model.put("poolLibraryMap", poolLibraryMap);
model.put("libraryPools", pools);
model.put("libraryRuns", getRunsByLibraryPools(pools));
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, library, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, library, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, library, securityManager.listAllGroups()));
model.put("title", "Library " + libraryId);
return new ModelAndView("/pages/editLibrary.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show library", ex);
}
throw ex;
}
}
@RequestMapping(value = "/{libraryId}/sample/{sampleId}", method = RequestMethod.GET)
public ModelAndView setupForm(@PathVariable Long libraryId,
@PathVariable Long sampleId,
ModelMap model) throws IOException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Library library = null;
if (libraryId == AbstractLibrary.UNSAVED_ID) {
library = dataObjectFactory.getLibrary(user);
model.put("title", "New Library");
}
else {
library = requestManager.getLibraryById(libraryId);
model.put("title", "Library " + libraryId);
if (library.getTagBarcodes() != null && !library.getTagBarcodes().isEmpty() && library.getTagBarcodes().get(1) != null) {
model.put("selectedTagBarcodeStrategy", library.getTagBarcodes().get(1).getStrategyName());
model.put("availableTagBarcodeStrategyBarcodes", tagBarcodeStrategyResolverService.getTagBarcodeStrategy(
library.getTagBarcodes().get(1).getStrategyName()).getApplicableBarcodes());
}
}
if (!library.userCanRead(user)) {
throw new SecurityException("Permission denied.");
}
if (sampleId != null) {
Sample sample = requestManager.getSampleById(sampleId);
model.put("sample", sample);
List<Sample> projectSamples = new ArrayList<Sample>(requestManager.listAllSamplesByProjectId(sample.getProject().getProjectId()));
Collections.sort(projectSamples, new AliasComparator(Sample.class));
model.put("projectSamples", projectSamples);
String regex = "([A-z0-9]+)_S([A-z0-9]+)_(.*)";
Pattern pat = Pattern.compile(regex);
Matcher mat = pat.matcher(sample.getAlias());
if (mat.matches()) {
//convert the sample alias automatically to a library alias
int numLibs = requestManager.listAllLibrariesBySampleId(sample.getId()).size();
String autogenLibAlias = mat.group(1) + "_" + "L" + mat.group(2) + "-"+(numLibs+1)+"_" + mat.group(3);
model.put("autogeneratedLibraryAlias", autogenLibAlias);
}
library.setSample(sample);
if (Arrays.asList(user.getRoles()).contains("ROLE_TECH")) {
SecurityProfile sp = new SecurityProfile(user);
LimsUtils.inheritUsersAndGroups(library, sample.getSecurityProfile());
sp.setOwner(user);
library.setSecurityProfile(sp);
}
else {
library.inheritPermissions(sample);
}
}
model.put("formObj", library);
model.put("library", library);
Collection<emPCR> pcrs = populateEmPcrs(user, library);
model.put("emPCRs", pcrs);
model.put("emPcrDilutions", populateEmPcrDilutions(user, pcrs));
model.put("availableTagBarcodeStrategies", populateAvailableTagBarcodeStrategies(library));
Map<String, Library> adjacentLibraries = getAdjacentLibrariesInProject(library, library.getSample().getProject());
if (!adjacentLibraries.isEmpty()) {
model.put("previousLibrary", adjacentLibraries.get("previousLibrary"));
model.put("nextLibrary", adjacentLibraries.get("nextLibrary"));
}
List<Pool<? extends Poolable>> pools = getPoolsByLibrary(library);
Map<Long, Library> poolLibraryMap = new HashMap<>();
for (Pool pool : pools) {
poolLibraryMap.put(pool.getId(), library);
}
model.put("poolLibraryMap", poolLibraryMap);
model.put("libraryPools", pools);
model.put("libraryRuns", getRunsByLibraryPools(pools));
model.put("owners", LimsSecurityUtils.getPotentialOwners(user, library, securityManager.listAllUsers()));
model.put("accessibleUsers", LimsSecurityUtils.getAccessibleUsers(user, library, securityManager.listAllUsers()));
model.put("accessibleGroups", LimsSecurityUtils.getAccessibleGroups(user, library, securityManager.listAllGroups()));
return new ModelAndView("/pages/editLibrary.jsp", model);
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to show library", ex);
}
throw ex;
}
catch (NoSuchMethodException e) {
if (log.isDebugEnabled()) {
log.debug("Failed to sort project samples", e);
}
throw new IOException(e);
}
}
@RequestMapping(method = RequestMethod.POST)
public String processSubmit(@ModelAttribute("library") Library library,
ModelMap model,
SessionStatus session) throws IOException, MalformedLibraryException {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
if (!library.userCanWrite(user)) {
throw new SecurityException("Permission denied.");
}
requestManager.saveLibrary(library);
session.setComplete();
model.clear();
return "redirect:/miso/library/" + library.getId();
}
catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to save library", ex);
}
throw ex;
}
}
}