/*
* 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.spring.ajax;
import com.eaglegenomics.simlims.core.Note;
import com.eaglegenomics.simlims.core.SecurityProfile;
import com.eaglegenomics.simlims.core.User;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import com.opensymphony.util.FileUtils;
import net.sf.json.JSONArray;
import net.sf.json.JSONException;
import net.sf.json.JSONObject;
import net.sourceforge.fluxion.ajax.Ajaxified;
import net.sourceforge.fluxion.ajax.util.JSONUtils;
import org.krysalis.barcode4j.BarcodeDimension;
import org.krysalis.barcode4j.BarcodeGenerator;
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.web.context.request.RequestContextHolder;
import org.springframework.web.context.request.ServletRequestAttributes;
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.LibraryImpl;
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.data.type.LibraryType;
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.MalformedSampleQcException;
import uk.ac.bbsrc.tgac.miso.core.exception.MisoNamingException;
import uk.ac.bbsrc.tgac.miso.core.exception.MisoPrintException;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.factory.barcode.BarcodeFactory;
import uk.ac.bbsrc.tgac.miso.core.factory.barcode.MisoJscriptFactory;
import uk.ac.bbsrc.tgac.miso.core.manager.FilesManager;
import uk.ac.bbsrc.tgac.miso.core.manager.MisoFilesManager;
import uk.ac.bbsrc.tgac.miso.core.manager.PrintManager;
import uk.ac.bbsrc.tgac.miso.core.manager.RequestManager;
import uk.ac.bbsrc.tgac.miso.core.service.naming.MisoNamingScheme;
import uk.ac.bbsrc.tgac.miso.core.service.printing.MisoPrintService;
import uk.ac.bbsrc.tgac.miso.core.service.printing.context.PrintContext;
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 javax.imageio.ImageIO;
import javax.servlet.http.HttpSession;
import java.awt.image.RenderedImage;
import java.io.File;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* uk.ac.bbsrc.tgac.miso.spring.ajax
* <p/>
* Info
*
* @author Rob Davey
* @since 0.0.2
*/
@Ajaxified
public class LibraryControllerHelperService {
protected static final Logger log = LoggerFactory.getLogger(LibraryControllerHelperService.class);
@Autowired
private SecurityManager securityManager;
@Autowired
private RequestManager requestManager;
@Autowired
private DataObjectFactory dataObjectFactory;
@Autowired
private BarcodeFactory barcodeFactory;
@Autowired
private MisoFilesManager misoFileManager;
@Autowired
private PrintManager<MisoPrintService, Queue<?>> printManager;
@Autowired
private TagBarcodeStrategyResolverService tagBarcodeStrategyResolverService;
@Autowired
private MisoNamingScheme<Sample> sampleNamingScheme;
@Autowired
private MisoNamingScheme<Library> libraryNamingScheme;
public JSONObject validateLibraryAlias(HttpSession session, JSONObject json) {
if (json.has("alias")) {
String alias = json.getString("alias");
try {
if (libraryNamingScheme.validateField("alias", alias)) {
log.debug("Library alias OK!");
return JSONUtils.SimpleJSONResponse("OK");
}
else {
log.error("Library alias not valid: " + alias);
return JSONUtils.SimpleJSONError("The following Library alias doesn't conform to the chosen naming scheme ("+libraryNamingScheme.getValidationRegex("alias")+") or already exists: " + json.getString("alias"));
}
}
catch (MisoNamingException e) {
log.error("Cannot validate Library alias " + json.getString("alias") + ": " + e.getMessage());
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot validate Library alias " + json.getString("alias") + ": " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("No alias specified");
}
}
public JSONObject addLibraryNote(HttpSession session, JSONObject json) {
Long libraryId = json.getLong("libraryId");
String internalOnly = json.getString("internalOnly");
String text = json.getString("text");
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Library library = requestManager.getLibraryById(libraryId);
Note note = new Note();
internalOnly = internalOnly.equals("on") ? "true" : "false";
note.setInternalOnly(Boolean.parseBoolean(internalOnly));
note.setText(text);
note.setOwner(user);
note.setCreationDate(new Date());
library.getNotes().add(note);
requestManager.saveLibraryNote(library, note);
requestManager.saveLibrary(library);
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage());
}
return JSONUtils.SimpleJSONResponse("Note saved successfully");
}
public JSONObject deleteLibraryNote(HttpSession session, JSONObject json) {
Long libraryId = json.getLong("libraryId");
Long noteId = json.getLong("noteId");
try {
Library library = requestManager.getLibraryById(libraryId);
Note note = requestManager.getNoteById(noteId);
if (library.getNotes().contains(note)) {
library.getNotes().remove(note);
requestManager.deleteNote(note);
requestManager.saveLibrary(library);
return JSONUtils.SimpleJSONResponse("OK");
}
else {
return JSONUtils.SimpleJSONError("Library does not have note " + noteId + ". Cannot remove");
}
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot remove note: " + e.getMessage());
}
}
public JSONObject getLibraryBarcode(HttpSession session, JSONObject json) {
Long libraryId = json.getLong("libraryId");
File temploc = new File(session.getServletContext().getRealPath("/")+"temp/");
try {
Library library = requestManager.getLibraryById(libraryId);
barcodeFactory.setPointPixels(1.5f);
barcodeFactory.setBitmapResolution(600);
RenderedImage bi = null;
if (json.has("barcodeGenerator")) {
BarcodeDimension dim = new BarcodeDimension(100, 100);
if (json.has("dimensionWidth") && json.has("dimensionHeight")) {
dim = new BarcodeDimension(json.getDouble("dimensionWidth"), json.getDouble("dimensionHeight"));
}
BarcodeGenerator bg = BarcodeFactory.lookupGenerator(json.getString("barcodeGenerator"));
if (bg != null) {
bi = barcodeFactory.generateBarcode(library, bg, dim);
}
else {
return JSONUtils.SimpleJSONError("'"+json.getString("barcodeGenerator") + "' is not a valid barcode generator type");
}
}
else {
bi = barcodeFactory.generateSquareDataMatrix(library, 400);
}
if (bi != null) {
File tempimage = misoFileManager.generateTemporaryFile("barcode-", ".png", temploc);
if (ImageIO.write(bi, "png", tempimage)) {
return JSONUtils.JSONObjectResponse("img", tempimage.getName());
}
return JSONUtils.SimpleJSONError("Writing temp image file failed.");
}
else {
return JSONUtils.SimpleJSONError("Library has no parseable barcode");
}
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage() + ": Cannot seem to generate temp file for barcode");
}
}
public JSONObject printLibraryBarcodes(HttpSession session, JSONObject json) {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
String serviceName = null;
if (json.has("serviceName")) { serviceName = json.getString("serviceName"); }
MisoPrintService<File, Barcodable, PrintContext<File>> mps = null;
if (serviceName == null) {
Collection<MisoPrintService> services = printManager.listPrintServicesByBarcodeableClass(Library.class);
if (services.size() == 1) {
mps = services.iterator().next();
}
else {
return JSONUtils.SimpleJSONError("No serviceName specified, but more than one available service able to print this barcode type.");
}
}
else {
mps = printManager.getPrintService(serviceName);
}
Queue<File> thingsToPrint = new LinkedList<File>();
JSONArray ls = JSONArray.fromObject(json.getString("libraries"));
for (JSONObject l : (Iterable<JSONObject>)ls) {
try {
Long libraryId = l.getLong("libraryId");
Library library = requestManager.getLibraryById(libraryId);
//autosave the barcode if none has been previously generated
if (library.getIdentificationBarcode() == null || "".equals(library.getIdentificationBarcode())) {
requestManager.saveLibrary(library);
}
File f = mps.getLabelFor(library);
if (f!=null) thingsToPrint.add(f);
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Error printing barcodes: " + e.getMessage());
}
}
PrintJob pj = printManager.print(thingsToPrint, mps.getName(), user);
return JSONUtils.SimpleJSONResponse("Job "+pj.getJobId()+" : Barcodes printed.");
}
catch (MisoPrintException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to print barcodes: " + e.getMessage());
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to print barcodes: " + e.getMessage());
}
}
public JSONObject printLibraryDilutionBarcodes(HttpSession session, JSONObject json) {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
String serviceName = null;
if (json.has("serviceName")) { serviceName = json.getString("serviceName"); }
MisoPrintService<File, Barcodable, PrintContext<File>> mps = null;
if (serviceName == null) {
Collection<MisoPrintService> services = printManager.listPrintServicesByBarcodeableClass(LibraryDilution.class);
if (services.size() == 1) {
mps = services.iterator().next();
}
else {
return JSONUtils.SimpleJSONError("No serviceName specified, but more than one available service able to print this barcode type.");
}
}
else {
mps = printManager.getPrintService(serviceName);
}
Queue<File> thingsToPrint = new LinkedList<File>();
JSONArray ls = JSONArray.fromObject(json.getString("dilutions"));
for (JSONObject l : (Iterable<JSONObject>)ls) {
try {
Long dilutionId = l.getLong("dilutionId");
// String platform = l.getString("platform");
LibraryDilution dilution = requestManager.getLibraryDilutionById(dilutionId);
//autosave the barcode if none has been previously generated
if (dilution.getIdentificationBarcode() == null || "".equals(dilution.getIdentificationBarcode())) {
requestManager.saveLibraryDilution(dilution);
}
File f = mps.getLabelFor(dilution);
if (f!=null) thingsToPrint.add(f);
thingsToPrint.add(f);
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Error printing barcodes: " + e.getMessage());
}
}
PrintJob pj = printManager.print(thingsToPrint, mps.getName(), user);
return JSONUtils.SimpleJSONResponse("Job "+pj.getJobId()+" : Barcodes printed.");
}
catch (MisoPrintException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to print barcodes: " + e.getMessage());
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to print barcodes: " + e.getMessage());
}
}
public JSONObject changeLibraryLocation(HttpSession session, JSONObject json) {
Long libraryId = json.getLong("libraryId");
String locationBarcode = json.getString("locationBarcode");
try {
String newLocation = LimsUtils.lookupLocation(locationBarcode);
if (newLocation != null) {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
Library library = requestManager.getLibraryById(libraryId);
String oldLocation = library.getLocationBarcode();
library.setLocationBarcode(newLocation);
Note note = new Note();
note.setInternalOnly(true);
note.setText("Location changed from " + oldLocation + " to " + newLocation + " by " + user.getLoginName() + " on " + new Date());
note.setOwner(user);
note.setCreationDate(new Date());
library.getNotes().add(note);
requestManager.saveLibraryNote(library, note);
requestManager.saveLibrary(library);
}
else {
return JSONUtils.SimpleJSONError("New location barcode not recognised");
}
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage());
}
return JSONUtils.SimpleJSONResponse("Note saved successfully");
}
public JSONObject getLibraryDilutionBarcode(HttpSession session, JSONObject json) {
Long dilutionId = json.getLong("dilutionId");
File temploc = new File(session.getServletContext().getRealPath("/")+"temp/");
try {
LibraryDilution dil = requestManager.getLibraryDilutionById(dilutionId);
barcodeFactory.setPointPixels(1.5f);
barcodeFactory.setBitmapResolution(600);
RenderedImage bi = barcodeFactory.generateSquareDataMatrix(dil, 400);
if (bi != null) {
File tempimage = misoFileManager.generateTemporaryFile("barcode-", ".png", temploc);
if (ImageIO.write(bi, "png", tempimage)) {
return JSONUtils.JSONObjectResponse("img", tempimage.getName());
}
return JSONUtils.SimpleJSONError("Writing temp image file failed.");
}
else {
return JSONUtils.SimpleJSONError("Dilution has no parseable barcode");
}
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage() + ": Cannot seem to generate temp file for barcode");
}
}
public JSONObject getBarcodesPositions(HttpSession session, JSONObject json) {
if (json.has("strategy")) {
TagBarcodeStrategy tbs = tagBarcodeStrategyResolverService.getTagBarcodeStrategy(json.getString("strategy"));
if (tbs != null) {
JSONObject j = new JSONObject();
j.put("numApplicableBarcodes", tbs.getNumApplicableBarcodes());
return j;
}
return JSONUtils.SimpleJSONError("No strategy found with the name: \"" + json.getString("strategy") + "\"");
}
else {
return JSONUtils.SimpleJSONError("No valid strategy given");
}
}
public JSONObject bulkSaveLibraries(HttpSession session, JSONObject json) {
if (json.has("libraries")) {
try {
Project p = requestManager.getProjectById(json.getLong("projectId"));
JSONArray a = JSONArray.fromObject(json.get("libraries"));
Set<Library> saveSet = new HashSet<Library>();
for (JSONObject j : (Iterable<JSONObject>) a) {
try {
SecurityProfile sp = null;
Sample sample = null;
//String libAlias = null;
String sampleAlias = j.getString("parentSample");
for (Sample s : p.getSamples()) {
if (s.getAlias().equals(sampleAlias)) {
sp = s.getSecurityProfile();
sample = s;
break;
/*
if (sampleNamingScheme.validateField("alias", s.getAlias())) {
Pattern pat = Pattern.compile(sampleNamingScheme.getValidationRegex("alias"));
Matcher mat = pat.matcher(s.getAlias());
//convert the sample alias automatically to a library alias
int numLibs = requestManager.listAllLibrariesBySampleId(s.getId()).size();
String la = mat.group(1) + "_" + "L" + mat.group(2) + "-"+(numLibs+1)+"_" + mat.group(3);
if (libraryNamingScheme.validateField("alias", la)) {
libAlias = la;
}
}*/
}
}
if (sample != null) { // && libAlias != null) {
String descr = j.getString("description");
String platform = j.getString("platform");
String type = j.getString("libraryType");
String selectionType = j.getString("selectionType");
String strategyType = j.getString("strategyType");
String locationBarcode = j.getString("locationBarcode");
Library library = new LibraryImpl();
library.setSample(sample);
String libAlias = libraryNamingScheme.generateNameFor("alias", library);
library.setAlias(libAlias);
library.setSecurityProfile(sp);
library.setDescription(descr);
library.setPlatformName(platform);
library.setCreationDate(new Date());
library.setLocationBarcode(locationBarcode);
library.setQcPassed(false);
library.setLibraryType(requestManager.getLibraryTypeByDescription(type));
library.setLibrarySelectionType(requestManager.getLibrarySelectionTypeByName(selectionType));
library.setLibraryStrategyType(requestManager.getLibraryStrategyTypeByName(strategyType));
boolean paired = false;
if (!"".equals(j.getString("paired"))) {
paired = j.getBoolean("paired");
}
library.setPaired(paired);
if (j.has("tagBarcodes") && !"".equals(j.getString("tagBarcodes")) && !j.getString("tagBarcodes").contains("Select")) {
String[] codes = j.getString("tagBarcodes").split(Pattern.quote("|"));
HashMap<Integer, TagBarcode> barcodes = new HashMap<Integer, TagBarcode>();
int count = 1;
for (String code : codes) {
try {
long cl = Long.parseLong(code);
barcodes.put(count, requestManager.getTagBarcodeById(cl));
}
catch (NumberFormatException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot save Library. It looks like there are tag barcodes for the library of "+sample.getAlias()+", but they cannot be processed");
}
finally {
count++;
}
}
library.setTagBarcodes(barcodes);
}
saveSet.add(library);
}
else {
throw new IOException("Could not process a selected Sample to generate Libraries. Please check that all selected samples' aliases conform to the chosen naming convention ("+sampleNamingScheme.getValidationRegex("alias")+")");
}
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot save Library generated from " + j.getString("parentSample") + ": " + e.getMessage());
}
catch (JSONException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot save Library. Something cannot be retrieved from the bulk input table: " + e.getMessage());
}
}
/*
Set<Library> complement = LimsUtils.relativeComplementByProperty(
Library.class,
"getAlias",
saveSet,
new HashSet(requestManager.listAllLibrariesByProjectId(json.getLong("projectId"))));
*/
List<Library> sortedList = new ArrayList<Library>(saveSet);
Collections.sort(sortedList, new AliasComparator(Library.class));
for (Library library : sortedList) {
requestManager.saveLibrary(library);
}
return JSONUtils.SimpleJSONResponse("All libraries saved successfully");
}
catch (Exception e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot retrieve parent project with ID " + json.getLong("projectId"));
}
}
else {
return JSONUtils.SimpleJSONError("No libraries specified");
}
}
public JSONObject changePlatformName(HttpSession session, JSONObject json) {
try {
if (json.has("platform") && !json.get("platform").equals("")) {
String platform = json.getString("platform");
Map<String, Object> map = new HashMap<String, Object>();
StringBuilder libsb = new StringBuilder();
List<LibraryType> types = new ArrayList<LibraryType>(requestManager.listLibraryTypesByPlatform(platform));
Collections.sort(types);
for (LibraryType s : types) {
libsb.append("<option value='" + s.getLibraryTypeId() + "'>"+s.getDescription()+"</option>");
}
StringBuilder tagsb = new StringBuilder();
List<TagBarcodeStrategy> strategies = new ArrayList<TagBarcodeStrategy>(tagBarcodeStrategyResolverService.getTagBarcodeStrategiesByPlatform(PlatformType.get(platform)));
tagsb.append("<option value=''>No Barcode Strategy</option>");
for (TagBarcodeStrategy tb : strategies) {
tagsb.append("<option value='" + tb.getName() + "'>"+tb.getName()+"</option>");
}
map.put("libraryTypes", libsb.toString());
map.put("tagBarcodeStrategies", tagsb.toString());
return JSONUtils.JSONObjectResponse(map);
}
}
catch (IOException e) {
e.printStackTrace();
log.error("Failed to retrieve library types given platform type: ", e);
return JSONUtils.SimpleJSONError("Failed to retrieve library types given platform type: " + e.getMessage());
}
return JSONUtils.SimpleJSONError("Cannot resolve LibraryType from selected Platform");
}
public JSONObject getTagBarcodesForStrategy(HttpSession session, JSONObject json) {
if (json.has("strategy")) {
TagBarcodeStrategy tbs = tagBarcodeStrategyResolverService.getTagBarcodeStrategy(json.getString("strategy"));
if (tbs != null) {
Map<String, Object> map = new HashMap<String, Object>();
Map<Integer, Set<TagBarcode>> barcodes = tbs.getApplicableBarcodes();
StringBuilder tagsb = new StringBuilder();
for (Integer i : barcodes.keySet()) {
//select
tagsb.append("Barcode "+i+": " + "<select id='tagBarcodes[\""+i+"\"]' name='tagBarcodes[\""+i+"\"]'>");
tagsb.append("<option value=''>No Barcode</option>");
List<TagBarcode> bs = new ArrayList<TagBarcode>(barcodes.get(i));
Collections.sort(bs);
for (TagBarcode tb : bs) {
//option
tagsb.append("<option value='" + tb.getId() + "'>"+tb.getName()+"</option>");
}
tagsb.append("</select><br/>");
tagsb.append("<input type='hidden' value='on' name='_tagBarcodes[\""+i+"\"]'/>");
}
map.put("tagBarcodes", tagsb.toString());
return JSONUtils.JSONObjectResponse(map);
}
else {
return JSONUtils.SimpleJSONError("No such TagBarcodeStrategy: " + json.getString("strategy"));
}
}
else {
return JSONUtils.SimpleJSONError("No valid TagBarcodeStrategy selected");
}
}
public JSONObject getLibraryQcTypes(HttpSession session, JSONObject json) {
try {
StringBuilder sb = new StringBuilder();
Collection<QcType> types = requestManager.listAllLibraryQcTypes();
for (QcType s : types) {
sb.append("<option units='"+s.getUnits()+"' value='" + s.getQcTypeId() + "'>"+s.getName()+"</option>");
}
Map<String, Object> map = new HashMap<String, Object>();
map.put("types", sb.toString());
return JSONUtils.JSONObjectResponse(map);
}
catch (IOException e) {
e.printStackTrace();
}
return JSONUtils.SimpleJSONError("Cannot list all Library QC Types");
}
public JSONObject addLibraryQC(HttpSession session, JSONObject json) {
try {
for (Object key : json.keySet()) {
if (json.get(key) == null || json.get(key).equals("")) {
String k = (String)key;
return JSONUtils.SimpleJSONError("Please enter a value for '" +k+ "'");
}
}
if (json.has("libraryId") && !json.get("libraryId").equals("")) {
Long libraryId = Long.parseLong(json.getString("libraryId"));
Library library = requestManager.getLibraryById(libraryId);
LibraryQC newQc = dataObjectFactory.getLibraryQC();
if (json.has("qcPassed") && json.getString("qcPassed").equals("true")) {
library.setQcPassed(true);
}
newQc.setQcCreator(json.getString("qcCreator"));
newQc.setQcDate(new SimpleDateFormat("dd/MM/yyyy").parse(json.getString("qcDate")));
newQc.setQcType(requestManager.getLibraryQcTypeById(json.getLong("qcType")));
newQc.setResults(Double.parseDouble(json.getString("results")));
newQc.setInsertSize(Integer.parseInt(json.getString("insertSize")));
library.addQc(newQc);
requestManager.saveLibraryQC(newQc);
StringBuilder sb = new StringBuilder();
//sb.append("<tr><th>ID</th><th>QCed By</th><th>QC Date</th><th>Method</th><th>Results</th><th>Insert Size</th></tr>");
sb.append("<tr><th>QCed By</th><th>QC Date</th><th>Method</th><th>Results</th><th>Insert Size</th></tr>");
for (LibraryQC qc : library.getLibraryQCs()) {
sb.append("<tr>");
//sb.append("<td>"+qc.getQcId()+"</td>");
sb.append("<td>"+qc.getQcCreator()+"</td>");
sb.append("<td>"+qc.getQcDate()+"</td>");
sb.append("<td>"+qc.getQcType().getName()+"</td>");
sb.append("<td>"+qc.getResults()+" "+ qc.getQcType().getUnits() +"</td>");
sb.append("<td>"+qc.getInsertSize()+" bp</td>");
sb.append("</tr>");
}
return JSONUtils.SimpleJSONResponse(sb.toString());
}
}
catch (Exception e) {
log.error("Failed to add Library QC to this Library: ", e);
return JSONUtils.SimpleJSONError("Failed to add Library QC to this Library: " + e.getMessage());
}
return JSONUtils.SimpleJSONError("Cannot add LibraryQC");
}
public JSONObject bulkAddLibraryQCs(HttpSession session, JSONObject json) {
try {
JSONArray qcs = JSONArray.fromObject(json.getString("qcs"));
//validate
boolean ok = true;
for (JSONObject qc : (Iterable<JSONObject>)qcs) {
String qcPassed = qc.getString("qcPassed");
String qcType = qc.getString("qcType");
String results = qc.getString("results");
String qcCreator = qc.getString("qcCreator");
String qcDate = qc.getString("qcDate");
String insertSize = qc.getString("insertSize");
//if (qcPassed == null || qcPassed.equals("") ||
if (qcType == null || qcType.equals("") ||
results == null || results.equals("") ||
qcCreator == null || qcCreator.equals("") ||
qcDate == null || qcDate.equals("") ||
insertSize == null || insertSize.equals("")) {
ok = false;
}
}
//persist
if (ok) {
Map<String, Object> map = new HashMap<String, Object>();
JSONArray a = new JSONArray();
JSONArray errors = new JSONArray();
for (JSONObject qc : (Iterable<JSONObject>)qcs) {
JSONObject j = addLibraryQC(session, qc);
j.put("libraryId", qc.getString("libraryId"));
if (j.has("error")) {
errors.add(j);
}
else {
a.add(j);
}
}
map.put("saved", a);
if (!errors.isEmpty()) {
map.put("errors", errors);
}
return JSONUtils.JSONObjectResponse(map);
}
else {
log.error("Failed to add Library QC to this Library: one of the required fields of the selected QCs is missing or invalid");
return JSONUtils.SimpleJSONError("Failed to add Library QC to this Library: one of the required fields of the selected QCs is missing or invalid");
}
}
catch (Exception e) {
log.error("Failed to add Library QC to this Library: ", e);
return JSONUtils.SimpleJSONError("Failed to add Library QC to this Library: " + e.getMessage());
}
}
public JSONObject addLibraryDilution(HttpSession session, JSONObject json) {
try {
for (Object key : json.keySet()) {
if (json.get(key) == null || json.get(key).equals("")) {
String k = (String)key;
return JSONUtils.SimpleJSONError("Please enter a value for '" +k+ "'");
}
}
if (json.has("libraryId") && !json.get("libraryId").equals("")) {
Long libraryId = Long.parseLong(json.getString("libraryId"));
Library library = requestManager.getLibraryById(libraryId);
LibraryDilution newDilution = dataObjectFactory.getLibraryDilution();
newDilution.setSecurityProfile(library.getSecurityProfile());
newDilution.setDilutionCreator(json.getString("dilutionCreator"));
newDilution.setCreationDate(new SimpleDateFormat("dd/MM/yyyy").parse(json.getString("dilutionDate")));
//newDilution.setLocationBarcode(json.getString("locationBarcode"));
newDilution.setConcentration(Double.parseDouble(json.getString("results")));
library.addDilution(newDilution);
requestManager.saveLibraryDilution(newDilution);
StringBuilder sb = new StringBuilder();
sb.append("<tr>");
//sb.append("<th>ID</th><th>Done By</th><th>Date</th><th>Barcode</th><th>Results</th>");
sb.append("<th>LD Name</th><th>Done By</th><th>Date</th><th>Results</th><th>ID barcode</th>");
if (!library.getPlatformName().equals("Illumina")) {
sb.append("<th>Add emPCR</th>");
}
sb.append("</tr>");
File temploc = new File(session.getServletContext().getRealPath("/")+"temp/");
for (LibraryDilution dil : library.getLibraryDilutions()) {
sb.append("<tr>");
sb.append("<td>"+dil.getName()+"</td>");
sb.append("<td>"+dil.getDilutionCreator()+"</td>");
sb.append("<td>"+dil.getCreationDate()+"</td>");
sb.append("<td>"+dil.getConcentration()+" "+ dil.getUnits()+"</td>");
sb.append("<td>");
try {
barcodeFactory.setPointPixels(1.5f);
barcodeFactory.setBitmapResolution(600);
RenderedImage bi = barcodeFactory.generateSquareDataMatrix(dil, 400);
if (bi != null) {
File tempimage = misoFileManager.generateTemporaryFile("barcode-", ".png", temploc);
if (ImageIO.write(bi, "png", tempimage)) {
sb.append("<img style='border:0;' src='/temp/"+tempimage.getName()+"'/>");
}
}
}
catch (IOException e) {
e.printStackTrace();
}
sb.append("</td>");
if (!library.getPlatformName().equals("Illumina")) {
sb.append("<td><a href='javascript:void(0);' onclick='Library.empcr.insertEmPcrRow("+dil.getId()+");'>Add emPCR</a></td>");
}
else {
//sb.append("<td><a href='/miso/poolwizard/new/"+library.getPlatformName().toLowerCase()+"/new/'>Construct New Pool</a></td>");
sb.append("<td><a href='/miso/poolwizard/new/"+library.getSample().getProject().getProjectId()+"'>Construct New Pool</a></td>");
}
sb.append("</tr>");
}
return JSONUtils.SimpleJSONResponse(sb.toString());
}
}
catch (Exception e) {
log.error("Failed to add Library Dilution to this Library: ", e);
return JSONUtils.SimpleJSONError("Failed to add Library Dilution to this Library: " + e.getMessage());
}
return JSONUtils.SimpleJSONError("Cannot add LibraryDilution");
}
public JSONObject bulkAddLibraryDilutions(HttpSession session, JSONObject json) {
try {
JSONArray dilutions = JSONArray.fromObject(json.getString("dilutions"));
//validate
boolean ok = true;
for (JSONObject dil : (Iterable<JSONObject>)dilutions) {
String results = dil.getString("results");
String dilutionCreator = dil.getString("dilutionCreator");
String dilutionDate = dil.getString("dilutionDate");
if (results == null || results.equals("") ||
dilutionCreator == null || dilutionCreator.equals("") ||
dilutionDate == null || dilutionDate.equals("")) {
ok = false;
}
}
//persist
if (ok) {
Map<String, Object> map = new HashMap<String, Object>();
JSONArray a = new JSONArray();
JSONArray errors = new JSONArray();
for (JSONObject dil : (Iterable<JSONObject>)dilutions) {
JSONObject j = addLibraryDilution(session, dil);
j.put("libraryId", dil.getString("libraryId"));
if (j.has("error")) {
errors.add(j);
}
else {
a.add(j);
}
}
map.put("saved", a);
if (!errors.isEmpty()) {
map.put("errors", errors);
}
return JSONUtils.JSONObjectResponse(map);
}
else {
log.error("Failed to add Library Dilutions to this Library: one of the required fields of the selected Library Dilutions is missing or invalid");
return JSONUtils.SimpleJSONError("Failed to add Library Dilutions to this Library: one of the required fields of the selected Library Dilutions is missing or invalid");
}
}
catch (Exception e) {
log.error("Failed to add Library Dilutions to this Library: ", e);
return JSONUtils.SimpleJSONError("Failed to add Library Dilutions to this Library: " + e.getMessage());
}
}
public JSONObject changeLibraryDilutionRow(HttpSession session, JSONObject json) {
try {
JSONObject response = new JSONObject();
Long dilutionId = Long.parseLong(json.getString("dilutionId"));
LibraryDilution dilution = requestManager.getLibraryDilutionById(dilutionId);
response.put("results", "<input type='text' id='" + dilutionId + "' value='" + dilution.getConcentration() + "'/>");
response.put("edit", "<a href='javascript:void(0);' onclick='Library.dilution.editLibraryDilution(\"" + dilutionId + "\");'>Save</a>");
return response;
}
catch (Exception e) {
log.error("Failed to display Library Dilution of this Library: ", e);
return JSONUtils.SimpleJSONError("Failed to display Library Dilution of this sample: " + e.getMessage());
}
}
public JSONObject editLibraryDilution(HttpSession session, JSONObject json) {
try {
if (json.has("dilutionId") && !json.get("dilutionId").equals("")) {
Long dilutionId = Long.parseLong(json.getString("dilutionId"));
LibraryDilution dilution = requestManager.getLibraryDilutionById(dilutionId);
dilution.setConcentration(Double.parseDouble(json.getString("result")));
requestManager.saveLibraryDilution(dilution);
return JSONUtils.SimpleJSONResponse("OK");
}
}
catch (Exception e) {
log.error("Failed to edit Library Dilution of this Library: ", e);
return JSONUtils.SimpleJSONError("Failed to edit Library Dilution of this Library: " + e.getMessage());
}
return JSONUtils.SimpleJSONError("Cannot add LibraryDilution");
}
public JSONObject addEmPcr(HttpSession session, JSONObject json) {
try {
for (Object key : json.keySet()) {
if (json.get(key) == null || json.get(key).equals("")) {
String k = (String)key;
return JSONUtils.SimpleJSONError("Please enter a value for '" +k+ "'");
}
}
if (json.has("dilutionId") && !json.get("dilutionId").equals("")) {
Long dilutionId = Long.parseLong(json.getString("dilutionId"));
LibraryDilution dilution = requestManager.getLibraryDilutionById(dilutionId);
emPCR pcr = dataObjectFactory.getEmPCR();
pcr.setSecurityProfile(dilution.getSecurityProfile());
pcr.setPcrCreator(json.getString("pcrCreator"));
pcr.setCreationDate(new SimpleDateFormat("dd/MM/yyyy").parse(json.getString("pcrDate")));
pcr.setConcentration(Double.parseDouble(json.getString("results")));
pcr.setLibraryDilution(dilution);
requestManager.saveEmPCR(pcr);
StringBuilder sb = new StringBuilder();
sb.append("<tr>");
sb.append("<th>ID</th><th>Done By</th><th>Date</th><th>Results</th>");
sb.append("<th>Add emPCR Dilution</th>");
sb.append("</tr>");
for (emPCR p : requestManager.listAllEmPCRsByDilutionId(dilutionId)) {
sb.append("<tr>");
sb.append("<td>"+p.getId()+"</td>");
sb.append("<td>"+p.getPcrCreator()+"</td>");
sb.append("<td>"+p.getCreationDate()+"</td>");
sb.append("<td>"+p.getConcentration()+" "+ p.getUnits()+"</td>");
sb.append("<td><a href='javascript:void(0);' onclick='Library.empcr.insertEmPcrDilutionRow("+p.getId()+");'>Add emPCR Dilution</a></td>");
sb.append("</tr>");
}
return JSONUtils.SimpleJSONResponse(sb.toString());
}
else {
log.error("Failed to add emPCR to this LibraryDilution: No parent Dilution ID found");
return JSONUtils.SimpleJSONError("Failed to add emPCR to this LibraryDilution: No parent Dilution ID found");
}
}
catch (Exception e) {
log.error("Failed to add emPCR to this LibraryDilution: ", e);
return JSONUtils.SimpleJSONError("Failed to add emPCR to this LibraryDilution: " + e.getMessage());
}
}
public JSONObject addEmPcrDilution(HttpSession session, JSONObject json) {
try {
for (Object key : json.keySet()) {
if (json.get(key) == null || json.get(key).equals("")) {
String k = (String)key;
return JSONUtils.SimpleJSONError("Please enter a value for '" +k+ "'");
}
}
if (json.has("pcrId") && !json.get("pcrId").equals("")) {
Long pcrId = Long.parseLong(json.getString("pcrId"));
emPCR pcr = requestManager.getEmPcrById(pcrId);
emPCRDilution newDilution = dataObjectFactory.getEmPCRDilution();
newDilution.setSecurityProfile(pcr.getSecurityProfile());
newDilution.setDilutionCreator(json.getString("pcrDilutionCreator"));
newDilution.setCreationDate(new SimpleDateFormat("dd/MM/yyyy").parse(json.getString("pcrDilutionDate")));
newDilution.setConcentration(Double.parseDouble(json.getString("results")));
newDilution.setEmPCR(pcr);
requestManager.saveEmPCRDilution(newDilution);
StringBuilder sb = new StringBuilder();
sb.append("<tr>");
//sb.append("<th>ID</th><th>Done By</th><th>Date</th><th>Barcode</th><th>Results</th>");
sb.append("<th>ID</th><th>Done By</th><th>Date</th><th>Results</th><th>ID Barcode</th>");
sb.append("</tr>");
File temploc = new File(session.getServletContext().getRealPath("/")+"temp/");
for (emPCRDilution dil : requestManager.listAllEmPcrDilutionsByEmPcrId(pcrId)) {
sb.append("<tr>");
sb.append("<td>"+dil.getId()+"</td>");
sb.append("<td>"+dil.getDilutionCreator()+"</td>");
sb.append("<td>"+dil.getCreationDate()+"</td>");
sb.append("<td>"+dil.getConcentration()+" "+ dil.getUnits()+"</td>");
sb.append("<td>");
try {
barcodeFactory.setPointPixels(1.5f);
barcodeFactory.setBitmapResolution(600);
RenderedImage bi = barcodeFactory.generateSquareDataMatrix(dil, 400);
if (bi != null) {
File tempimage = misoFileManager.generateTemporaryFile("barcode-", ".png", temploc);
if (ImageIO.write(bi, "png", tempimage)) {
sb.append("<img style='border:0;' src='/temp/"+tempimage.getName()+"'/>");
}
}
}
catch (IOException e) {
e.printStackTrace();
}
sb.append("</td>");
//sb.append("<td><a href='/miso/pool/"+pcr.getLibraryDilution().getLibrary().getPlatformName().toLowerCase()+"/new/'>Construct New Pool</a></td>");
sb.append("<td><a href='/miso/poolwizard/new/"+pcr.getLibraryDilution().getLibrary().getSample().getProject().getProjectId()+"'>Construct New Pool</a></td>");
sb.append("</tr>");
}
return JSONUtils.SimpleJSONResponse(sb.toString());
}
}
catch (Exception e) {
log.error("Failed to add EmPCRDilution to this EmPCR: ", e);
return JSONUtils.SimpleJSONError("Failed to add EmPCRDilution to this EmPCR: " + e.getMessage());
}
return JSONUtils.SimpleJSONError("Cannot add EmPCRDilution");
}
public JSONObject bulkAddEmPcrs(HttpSession session, JSONObject json) {
try {
JSONArray pcrs = JSONArray.fromObject(json.getString("pcrs"));
//validate
boolean ok = true;
for (JSONObject pcr : (Iterable<JSONObject>)pcrs) {
String pcrCreator = pcr.getString("pcrCreator");
String pcrDate = pcr.getString("pcrDate");
String concentration = pcr.getString("results");
if (concentration == null || concentration.equals("") ||
pcrCreator == null || pcrCreator.equals("") ||
pcrDate == null || pcrDate.equals("")) {
ok = false;
}
}
//persist
if (ok) {
Map<String, Object> map = new HashMap<String, Object>();
JSONArray a = new JSONArray();
JSONArray errors = new JSONArray();
for (JSONObject pcr : (Iterable<JSONObject>)pcrs) {
JSONObject j = addEmPcr(session, pcr);
j.put("dilutionId", pcr.getString("dilutionId"));
if (j.has("error")) {
errors.add(j);
}
else {
a.add(j);
}
}
map.put("saved", a);
if (!errors.isEmpty()) {
map.put("errors", errors);
}
return JSONUtils.JSONObjectResponse(map);
}
else {
log.error("Failed to add EmPCRs to this Library Dilution: one of the required fields of the selected EmPCR is missing or invalid");
return JSONUtils.SimpleJSONError("Failed to add EmPCRs to this Library Dilution: one of the required fields of the EmPCR is missing or invalid");
}
}
catch (Exception e) {
log.error("Failed to add EmPCRs to this Library Dilution: ", e);
return JSONUtils.SimpleJSONError("Failed to add EmPCRs to this Library Dilution: " + e.getMessage());
}
}
public JSONObject bulkAddEmPcrDilutions(HttpSession session, JSONObject json) {
try {
JSONArray dilutions = JSONArray.fromObject(json.getString("dilutions"));
//validate
boolean ok = true;
for (JSONObject dil : (Iterable<JSONObject>)dilutions) {
String dilutionCreator = dil.getString("pcrDilutionCreator");
String dilutionDate = dil.getString("pcrDilutionDate");
String concentration = dil.getString("results");
if (concentration == null || concentration.equals("") ||
dilutionCreator == null || dilutionCreator.equals("") ||
dilutionDate == null || dilutionDate.equals("")) {
ok = false;
}
}
//persist
if (ok) {
Map<String, Object> map = new HashMap<String, Object>();
JSONArray a = new JSONArray();
JSONArray errors = new JSONArray();
for (JSONObject dil : (Iterable<JSONObject>)dilutions) {
JSONObject j = addEmPcrDilution(session, dil);
j.put("pcrId", dil.getString("pcrId"));
if (j.has("error")) {
errors.add(j);
}
else {
a.add(j);
}
}
map.put("saved", a);
if (!errors.isEmpty()) {
map.put("errors", errors);
}
return JSONUtils.JSONObjectResponse(map);
}
else {
log.error("Failed to add EmPCR Dilutions to this EmPCR: one of the required fields of the selected EmPCR Dilutions is missing or invalid");
return JSONUtils.SimpleJSONError("Failed to add EmPCR Dilutions to this EmPCR: one of the required fields of the selected EmPCR Dilutions is missing or invalid");
}
}
catch (Exception e) {
log.error("Failed to add EmPCR Dilutions to this EmPCR: ", e);
return JSONUtils.SimpleJSONError("Failed to add EmPCR Dilutions to this EmPCR: " + e.getMessage());
}
}
public JSONObject changeLibraryQCRow(HttpSession session, JSONObject json) {
try {
JSONObject response = new JSONObject();
Long qcId = Long.parseLong(json.getString("qcId"));
LibraryQC libraryQc = requestManager.getLibraryQCById(qcId);
Long libraryId = Long.parseLong(json.getString("libraryId"));
response.put("results", "<input type='text' id='results" + qcId + "' value='" + libraryQc.getResults() + "'/>");
response.put("insertSize", "<input type='text' id='insertSize" + qcId + "' value='" + libraryQc.getInsertSize() + "'/>");
response.put("edit", "<a href='javascript:void(0);' onclick='Library.qc.editLibraryQC(\"" + qcId + "\",\"" + libraryId + "\");'>Save</a>");
return response;
}
catch (Exception e) {
log.error("Failed to display library QC of this library: ", e);
return JSONUtils.SimpleJSONError("Failed to display library QC of this library: " + e.getMessage());
}
}
public JSONObject editLibraryQC(HttpSession session, JSONObject json) {
try {
if (json.has("qcId") && !json.get("qcId").equals("")) {
Long qcId = Long.parseLong(json.getString("qcId"));
LibraryQC libraryQc = requestManager.getLibraryQCById(qcId);
libraryQc.setResults(Double.parseDouble(json.getString("result")));
libraryQc.setInsertSize(Integer.parseInt(json.getString("insertSize")));
requestManager.saveLibraryQC(libraryQc);
}
return JSONUtils.SimpleJSONResponse("done");
}
catch (Exception e) {
log.error("Failed to add library QC to this library: ", e);
return JSONUtils.SimpleJSONError("Failed to add library QC to this library: " + e.getMessage());
}
}
public JSONObject deleteLibrary(HttpSession session, JSONObject json) {
User user;
try {
user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Error getting currently logged in user.");
}
if (user != null && user.isAdmin()) {
if (json.has("libraryId")) {
Long libraryId = json.getLong("libraryId");
try {
requestManager.deleteLibrary(requestManager.getLibraryById(libraryId));
return JSONUtils.SimpleJSONResponse("Library deleted");
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot delete library: " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("No library specified to delete.");
}
}
else {
return JSONUtils.SimpleJSONError("Only logged-in admins can delete objects.");
}
}
public JSONObject deleteLibraryDilution(HttpSession session, JSONObject json) {
User user;
try {
user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Error getting currently logged in user.");
}
if (user != null && user.isAdmin()) {
if (json.has("libraryDilutionId")) {
Long libraryDilutionId = json.getLong("libraryDilutionId");
try {
requestManager.deleteLibraryDilution(requestManager.getLibraryDilutionById(libraryDilutionId));
return JSONUtils.SimpleJSONResponse("LibraryDilution deleted");
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot delete library dilution: " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("No library dilution specified to delete.");
}
}
else {
return JSONUtils.SimpleJSONError("Only logged-in admins can delete objects.");
}
}
public JSONObject deleteEmPCR(HttpSession session, JSONObject json) {
User user;
try {
user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Error getting currently logged in user.");
}
if (user != null && user.isAdmin()) {
if (json.has("empcrId")) {
Long empcrId = json.getLong("empcrId");
try {
requestManager.deleteEmPCR(requestManager.getEmPcrById(empcrId));
return JSONUtils.SimpleJSONResponse("EmPCR deleted");
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot delete EmPCR: " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("No EmPCR specified to delete.");
}
}
else {
return JSONUtils.SimpleJSONError("Only logged-in admins can delete objects.");
}
}
public JSONObject deleteEmPCRDilution(HttpSession session, JSONObject json) {
User user;
try {
user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Error getting currently logged in user.");
}
if (user != null && user.isAdmin()) {
if (json.has("deleteEmPCRDilution")) {
Long deleteEmPCRDilution = json.getLong("deleteEmPCRDilution");
try {
requestManager.deleteEmPcrDilution(requestManager.getEmPcrDilutionById(deleteEmPCRDilution));
return JSONUtils.SimpleJSONResponse("EmPCRDilution deleted");
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot delete EmPCR dilution: " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("No EmPCR dilution specified to delete.");
}
}
else {
return JSONUtils.SimpleJSONError("Only logged-in admins can delete objects.");
}
}
public JSONObject listLibrariesDataTable(HttpSession session, JSONObject json) {
try {
JSONObject j = new JSONObject();
JSONArray jsonArray = new JSONArray();
for (Library library : requestManager.listAllLibraries()) {
String qcpassed = "Unknown";
if (library.getQcPassed() != null) {
qcpassed = library.getQcPassed().toString();
}
jsonArray.add("['" + library.getName() + "','" +
library.getAlias() + "','" +
library.getLibraryType().getDescription() + "','" +
library.getSample().getName()+ "','" +
qcpassed + "','" +
"<a href=\"/miso/library/" + library.getId() + "\"><span class=\"ui-icon ui-icon-pencil\"></span></a>" + "']");
}
j.put("array", jsonArray);
return j;
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public void setSecurityManager(SecurityManager securityManager) {
this.securityManager = securityManager;
}
public void setRequestManager(RequestManager requestManager) {
this.requestManager = requestManager;
}
public void setDataObjectFactory(DataObjectFactory dataObjectFactory) {
this.dataObjectFactory = dataObjectFactory;
}
public void setBarcodeFactory(BarcodeFactory barcodeFactory) {
this.barcodeFactory = barcodeFactory;
}
public void setMisoFileManager(MisoFilesManager misoFileManager) {
this.misoFileManager = misoFileManager;
}
public void setPrintManager(PrintManager<MisoPrintService, Queue<?>> printManager) {
this.printManager = printManager;
}
public void setTagBarcodeStrategyResolverService(TagBarcodeStrategyResolverService tagBarcodeStrategyResolverService) {
this.tagBarcodeStrategyResolverService = tagBarcodeStrategyResolverService;
}
public void setSampleNamingScheme(MisoNamingScheme<Sample> sampleNamingScheme) {
this.sampleNamingScheme = sampleNamingScheme;
}
public void setLibraryNamingScheme(MisoNamingScheme<Library> libraryNamingScheme) {
this.libraryNamingScheme = libraryNamingScheme;
}
}