/*
* 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.fasterxml.jackson.databind.ObjectMapper;
import net.sf.json.JSONArray;
import org.codehaus.jackson.map.ObjectMapper;
import uk.ac.bbsrc.tgac.miso.core.data.*;
import com.eaglegenomics.simlims.core.User;
import com.eaglegenomics.simlims.core.manager.SecurityManager;
import net.sf.json.JSONObject;
import net.sourceforge.fluxion.ajax.Ajaxified;
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.security.core.context.SecurityContextHolder;
import uk.ac.bbsrc.tgac.miso.core.data.impl.*;
import uk.ac.bbsrc.tgac.miso.core.event.manager.WatchManager;
import uk.ac.bbsrc.tgac.miso.core.exception.MisoPrintException;
import uk.ac.bbsrc.tgac.miso.core.manager.IssueTrackerManager;
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.printing.MisoPrintService;
import uk.ac.bbsrc.tgac.miso.core.service.printing.context.PrintContext;
import uk.ac.bbsrc.tgac.miso.core.util.FormUtils;
import uk.ac.bbsrc.tgac.miso.core.util.LimsUtils;
import javax.servlet.http.HttpSession;
import java.io.File;
import java.io.IOException;
import java.util.*;
/**
* uk.ac.bbsrc.tgac.miso.spring.ajax
* <p/>
* Info
*
* @author Rob Davey
* @since 0.0.2
*/
@Ajaxified
public class ProjectControllerHelperService {
protected static final Logger log = LoggerFactory.getLogger(ProjectControllerHelperService.class);
@Autowired
private SecurityManager securityManager;
@Autowired
private RequestManager requestManager;
@Autowired
private IssueTrackerManager issueTrackerManager;
@Autowired
private PrintManager<MisoPrintService, Queue<?>> printManager;
@Autowired
private MisoFilesManager misoFileManager;
@Autowired
private WatchManager watchManager;
public void setSecurityManager(SecurityManager securityManager) {
this.securityManager = securityManager;
}
public void setRequestManager(RequestManager requestManager) {
this.requestManager = requestManager;
}
public void setIssueTrackerManager(IssueTrackerManager issueTrackerManager) {
this.issueTrackerManager = issueTrackerManager;
}
public void setMisoFileManager(MisoFilesManager misoFileManager) {
this.misoFileManager = misoFileManager;
}
public void setPrintManager(PrintManager<MisoPrintService, Queue<?>> printManager) {
this.printManager = printManager;
}
public void setWatchManager(WatchManager watchManager) {
this.watchManager = watchManager;
}
public JSONObject addProjectOverview(HttpSession session, JSONObject json) {
Long projectId = json.getLong("projectId");
String principalInvestigator = (String) json.get("principalInvestigator");
Integer numProposedSamples = json.getInt("numProposedSamples");
try {
Project project = requestManager.getProjectById(projectId);
ProjectOverview overview = new ProjectOverview();
overview.setNumProposedSamples(numProposedSamples);
overview.setPrincipalInvestigator(principalInvestigator);
overview.setProject(project);
overview.setLocked(false);
project.getOverviews().add(overview);
requestManager.saveProjectOverview(overview);
requestManager.saveProject(project);
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage());
}
return JSONUtils.SimpleJSONResponse("ok");
}
public JSONObject addProjectOverviewNote(HttpSession session, JSONObject json) {
Long overviewId = json.getLong("overviewId");
String internalOnly = json.getString("internalOnly");
String text = json.getString("text");
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
ProjectOverview overview = requestManager.getProjectOverviewById(overviewId);
Project project = overview.getProject();
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());
overview.getNotes().add(note);
requestManager.saveProjectOverviewNote(overview, note);
requestManager.saveProject(project);
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage());
}
return JSONUtils.SimpleJSONResponse("ok");
}
public JSONObject deleteProjectOverviewNote(HttpSession session, JSONObject json) {
Long overviewId = json.getLong("overviewId");
Long noteId = json.getLong("noteId");
try {
ProjectOverview po = requestManager.getProjectOverviewById(overviewId);
Note note = requestManager.getNoteById(noteId);
if (po.getNotes().contains(note)) {
po.getNotes().remove(note);
requestManager.deleteNote(note);
requestManager.saveProjectOverview(po);
return JSONUtils.SimpleJSONResponse("OK");
}
else {
return JSONUtils.SimpleJSONError("Project Overview does not have note " + noteId + ". Cannot remove");
}
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot remove note: " + e.getMessage());
}
}
public JSONObject unlockProjectOverview(HttpSession session, JSONObject json) {
Long overviewId = json.getLong("overviewId");
try {
ProjectOverview overview = requestManager.getProjectOverviewById(overviewId);
overview.setLocked(false);
requestManager.saveProjectOverview(overview);
requestManager.saveProject(overview.getProject());
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage());
}
return JSONUtils.SimpleJSONResponse("ok");
}
public JSONObject lockProjectOverview(HttpSession session, JSONObject json) {
Long overviewId = json.getLong("overviewId");
try {
ProjectOverview overview = requestManager.getProjectOverviewById(overviewId);
overview.setLocked(true);
requestManager.saveProjectOverview(overview);
requestManager.saveProject(overview.getProject());
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage());
}
return JSONUtils.SimpleJSONResponse("ok");
}
public JSONObject previewIssues(HttpSession session, JSONObject json) {
if (issueTrackerManager != null) {
List<JSONObject> issueList = new ArrayList<JSONObject>();
List<String> errorList = new ArrayList<String>();
JSONArray issues = JSONArray.fromObject(json.getString("issues"));
for (JSONObject issueKey : (Iterable<JSONObject>) issues) {
JSONObject issue = null;
try {
issue = issueTrackerManager.getIssue(issueKey.getString("key"));
if (issue != null) {
issueList.add(issue);
}
else {
errorList.add(issueKey.getString("key"));
}
}
catch (IOException e) {
e.printStackTrace();
errorList.add(issueKey.getString("key"));
}
}
JSONObject j = new JSONObject();
j.put("validIssues", JSONArray.fromObject(issueList));
j.put("invalidIssues", JSONArray.fromObject(errorList));
return j;
}
else {
return JSONUtils.SimpleJSONError("No issue tracker manager available.");
}
}
public JSONObject getIssues(HttpSession session, JSONObject json) {
if (issueTrackerManager != null) {
Long projectId = json.getLong("projectId");
try {
Project project = requestManager.getProjectById(projectId);
JSONObject j = new JSONObject();
if (project != null) {
List<JSONObject> issueList = new ArrayList<JSONObject>();
if (project.getIssueKeys() != null) {
for (String issueKey : project.getIssueKeys()) {
JSONObject issue = issueTrackerManager.getIssue(issueKey);
if (issue != null) {
issueList.add(issue);
}
}
j.put("issues", JSONArray.fromObject(issueList));
}
}
return j;
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("No issue tracker manager available.");
}
}
public JSONObject listProjectTrafficLight(HttpSession session, JSONObject json) {
try {
JSONObject j = new JSONObject();
for (Project project : requestManager.listAllProjects()) {
j.put(project.getProjectId(), checkOverviews(project.getProjectId()));
}
return j;
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject checkOverviewByProjectId(HttpSession session, JSONObject json) {
try {
JSONObject j = new JSONObject();
Long projectId = json.getLong("projectId");
j.put("response", checkOverviews(projectId));
return j;
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
private String checkOverviews(Long projectId) throws IOException {
StringBuilder sb = new StringBuilder();
Collection<ProjectOverview> overviews = requestManager.listAllOverviewsByProjectId(projectId);
if (overviews.size() > 0) {
sb.append("<table class=\"overviewSummary\">");
for (ProjectOverview overview : overviews) {
sb.append("<tr>");
sb.append("<td class=\"smallbox" + colorOverviewState(overview.getAllSampleQcPassed()) + "\">SQ</td>");
sb.append("<td class=\"smallbox" + colorOverviewState(overview.getLibraryPreparationComplete()) + "\">L</td>");
sb.append("<td class=\"smallbox" + colorOverviewState(overview.getAllLibrariesQcPassed()) + "\">LQ</td>");
sb.append("<td class=\"smallbox" + colorOverviewState(overview.getAllPoolsConstructed()) + "\">P</td>");
sb.append("<td class=\"smallbox" + colorOverviewState(overview.getAllRunsCompleted()) + "\">R</td>");
sb.append("<td class=\"smallbox" + colorOverviewState(overview.getPrimaryAnalysisCompleted()) + "\">A</td>");
sb.append("</tr>");
}
sb.append("</table>");
}
else {
sb.append("No Overview");
}
return sb.toString();
}
public JSONObject listProjectsDataTable(HttpSession session, JSONObject json) {
try {
JSONObject j = new JSONObject();
JSONArray jsonArray = new JSONArray();
for (Project project : requestManager.listAllProjects()) {
jsonArray.add("['" + project.getName() + "','" +
project.getAlias() + "','" +
project.getDescription() + "','" +
project.getProgress().getKey() + "','" +
// checkOverviews(project.getProjectId()) + "','" +
project.getProjectId() + "','" +
"<a href=\"/miso/project/" + project.getId() + "\"><span class=\"ui-icon ui-icon-pencil\"></span></a>" + "']");
}
j.put("projectsArray", jsonArray);
return j;
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
private String colorOverviewState(Boolean bool) {
if (bool) {
return " partitionOccupied";
}
else {
return "";
}
}
private String checkSamples(Long projectId) throws IOException {
Collection<Sample> samples = requestManager.listAllSamplesByProjectId(projectId);
if (samples.size() > 0) {
int pass = 0;
for (Sample s : samples) {
if (s.getQcPassed() != null) {
if (s.getQcPassed()) {
pass++;
}
}
}
if (pass == samples.size()) {
return "green";
}
else {
return "yellow";
}
}
else {
return "gray";
}
}
private String checkLibraries(Long projectId) throws IOException {
int pass = 0;
Collection<Library> libs = requestManager.listAllLibrariesByProjectId(projectId);
if (libs.size() > 0) {
for (Library l : libs) {
if (l.getLibraryQCs().size() > 0) {
pass += l.getLibraryQCs().size();
}
}
if (pass >= libs.size()) {
return "green";
}
else {
return "yellow";
}
}
else {
return "gray";
}
}
private String checkRuns(Long projectId) throws IOException {
int pass = 0;
Collection<Run> runs = requestManager.listAllRunsByProjectId(projectId);
if (runs.size() > 0) {
for (Run run : runs) {
if (run.getStatus() != null && run.getStatus().getHealth() != null && run.getStatus().getHealth().getKey().equals("Completed")) {
pass++;
}
}
if (pass == runs.size()) {
return "green";
}
else {
return "yellow";
}
}
else {
return "gray";
}
}
public JSONObject editProjectTrafficLight(HttpSession session, JSONObject json) {
Long projectId = json.getLong("projectId");
StringBuffer b = new StringBuffer();
try {
String trafSample = checkSamples(projectId);
String trafLib = checkLibraries(projectId);
String trafRun = checkRuns(projectId);
b.append("<div id=\"projectstatustrafficlight\">\n" +
" <table class=\"traf\">\n" +
"<thead><tr><th width=\"33%\">Samples</th><th width=\"33%\">Libraries</th><th width=\"33%\">Runs</th></tr></thead>" +
" <tbody>\n" +
" <tr>\n" +
" <td width=\"33%\"><img src=\"/styles/images/status/" + trafSample + ".png\"/></td>\n" +
" <td width=\"33%\"><img src=\"/styles/images/status/" + trafLib + ".png\"/></td>\n" +
" <td width=\"33%\"><img src=\"/styles/images/status/" + trafRun + ".png\"/></td>\n" +
" </tr>\n" +
" </tbody>\n" +
" </table>\n" +
"</div>");
return JSONUtils.JSONObjectResponse("html", b.toString());
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject printAllSampleBarcodes(HttpSession session, JSONObject json) {
Long projectId = json.getLong("projectId");
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(Sample.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>();
Collection<Sample> samples = requestManager.listAllSamplesByProjectId(projectId);
for (Sample sample : samples) {
//autosave the barcode if none has been previously generated
if (sample.getIdentificationBarcode() == null || "".equals(sample.getIdentificationBarcode())) {
requestManager.saveSample(sample);
}
File f = mps.getLabelFor(sample);
if (f != null) thingsToPrint.add(f);
}
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 printSelectedSampleBarcodes(HttpSession session, JSONObject json) {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
JSONArray ss = JSONArray.fromObject(json.getString("samples"));
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(Sample.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>();
for (JSONObject p : (Iterable<JSONObject>) ss) {
Long sampleId = p.getLong("sampleId");
Sample sample = requestManager.getSampleById(sampleId);
if (sample.getIdentificationBarcode() == null || "".equals(sample.getIdentificationBarcode())) {
requestManager.saveSample(sample);
}
File f = mps.getLabelFor(sample);
if (f != null) thingsToPrint.add(f);
}
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 printAllLibraryBarcodes(HttpSession session, JSONObject json) {
Long projectId = json.getLong("projectId");
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>();
Collection<Library> libraries = requestManager.listAllLibrariesByProjectId(projectId);
for (Library library : libraries) {
//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);
}
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 printSelectedLibraryBarcodes(HttpSession session, JSONObject json) {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
JSONArray ss = JSONArray.fromObject(json.getString("libraries"));
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>();
for (JSONObject p : (Iterable<JSONObject>) ss) {
Long libraryId = p.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);
}
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 printAllLibraryDilutionBarcodes(HttpSession session, JSONObject json) {
Long projectId = json.getLong("projectId");
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(Dilution.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>();
Collection<LibraryDilution> libraryDilutions = requestManager.listAllLibraryDilutionsByProjectId(projectId);
for (LibraryDilution libraryDilution : libraryDilutions) {
//autosave the barcode if none has been previously generated
if (libraryDilution.getIdentificationBarcode() == null || "".equals(libraryDilution.getIdentificationBarcode())) {
requestManager.saveLibraryDilution(libraryDilution);
}
File f = mps.getLabelFor(libraryDilution);
if (f != null) thingsToPrint.add(f);
}
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 printSelectedLibraryDilutionBarcodes(HttpSession session, JSONObject json) {
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
JSONArray ss = JSONArray.fromObject(json.getString("dilutions"));
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(Dilution.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>();
for (JSONObject p : (Iterable<JSONObject>) ss) {
Long dilutionId = p.getLong("dilutionId");
LibraryDilution libraryDilution = requestManager.getLibraryDilutionById(dilutionId);
//autosave the barcode if none has been previously generated
if (libraryDilution.getIdentificationBarcode() == null || "".equals(libraryDilution.getIdentificationBarcode())) {
requestManager.saveLibraryDilution(libraryDilution);
}
File f = mps.getLabelFor(libraryDilution);
if (f != null) thingsToPrint.add(f);
}
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 generateSampleDeliveryForm(HttpSession session, JSONObject json) {
Boolean plate = false;
if ("yes".equals(json.getString("plate"))){
plate = true;
}
Long projectId = json.getLong("projectId");
List<Sample> samples = new ArrayList<Sample>();
if (json.has("samples")) {
try {
JSONArray a = JSONArray.fromObject(json.get("samples"));
for (JSONObject j : (Iterable<JSONObject>) a) {
samples.add(requestManager.getSampleById(j.getLong("sampleId")));
}
File f = misoFileManager.getNewFile(
Project.class,
projectId.toString(),
"SampleInformationForm-" + LimsUtils.getCurrentDateAsString() + ".odt");
FormUtils.createSampleDeliveryForm(samples, f, plate);
return JSONUtils.SimpleJSONResponse("" + f.getName().hashCode());
}
catch (Exception e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to create sample delivery form: " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("No samples selected to generate delivery form");
}
}
public JSONObject downloadBulkSampleInputForm(HttpSession session, JSONObject json) {
if (json.has("projectId") && json.has("documentFormat")) {
Long projectId = json.getLong("projectId");
String documentFormat = json.getString("documentFormat");
try {
File f = misoFileManager.getNewFile(
Project.class,
projectId.toString(),
"BulkInputForm-" + LimsUtils.getCurrentDateAsString() + "." + documentFormat);
FormUtils.createSampleInputSpreadsheet(requestManager.getProjectById(projectId).getSamples(), f);
return JSONUtils.SimpleJSONResponse("" + f.getName().hashCode());
}
catch (Exception e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to get bulk input form: " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("Missing project ID or document format supplied.");
}
}
public JSONObject visualiseBulkSampleInputForm(HttpSession session, JSONObject json) {
JSONObject samplelist = (JSONObject) session.getAttribute("bulksamples");
if (samplelist == null) {
JSONObject error = (JSONObject) session.getAttribute("bulkerror");
if (error != null) {
return JSONUtils.SimpleJSONError("Failed to get bulk input sheet from session: " + error.getString("bulkerror"));
}
return JSONUtils.SimpleJSONError("Failed to get bulk input sheet from session.");
}
JSONArray samples = samplelist.getJSONArray("bulksamples");
if (samples != null) {
StringBuilder sb = new StringBuilder();
sb.append("<div style='width: 100%;'>");
ObjectMapper mapper = new ObjectMapper();
for (JSONObject sam : (Iterable<JSONObject>) samples) {
Sample s = null;
try {
s = mapper.readValue(sam.toString(), SampleImpl.class);
sb.append("<a class=\"dashboardresult\" href=\"/miso/sample/" + s.getId() + "\"><div onMouseOver=\"this.className='dashboardhighlight'\" onMouseOut=\"this.className='dashboard'\" class=\"dashboard\">");
sb.append("Name: <b>" + s.getName() + "</b><br/>");
sb.append("Alias: <b>" + s.getAlias() + "</b><br/>");
Set<Pool> pools = new HashSet<Pool>();
for (Library l : s.getLibraries()) {
if (!l.getLibraryDilutions().isEmpty()) {
for (Dilution ld : l.getLibraryDilutions()) {
if (!ld.getPools().isEmpty()) {
pools.addAll(ld.getPools());
}
}
}
}
if (!pools.isEmpty()) {
sb.append("Pools: <ul>");
for (Pool p : pools) {
sb.append("<li>")
.append(p.getName())
.append(" (")
.append(p.getAlias())
.append(") - ")
.append(p.getDilutions().size())
.append(" dilutions<li>");
}
sb.append("</ul><br/>");
}
sb.append("</div></a>");
}
catch (IOException e) {
e.printStackTrace();
}
finally {
sb.append("</div>");
session.removeAttribute("bulksamples");
}
}
return JSONUtils.SimpleJSONResponse(sb.toString());
}
else {
return JSONUtils.SimpleJSONError("Failed to get bulk input sheet from session.");
}
}
public JSONObject downloadPlateInputForm(HttpSession session, JSONObject json) {
if (json.has("projectId") && json.has("documentFormat")) {
Long projectId = json.getLong("projectId");
String documentFormat = json.getString("documentFormat");
try {
File f = misoFileManager.getNewFile(
Project.class,
projectId.toString(),
"PlateInputForm-" + LimsUtils.getCurrentDateAsString() + "." + documentFormat);
//TODO select a single sample to base sheet on?
FormUtils.createPlateInputSpreadsheet(f);
return JSONUtils.SimpleJSONResponse("" + f.getName().hashCode());
}
catch (Exception e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to get plate input form: " + e.getMessage());
}
}
else {
return JSONUtils.SimpleJSONError("Missing project ID or document format supplied.");
}
}
public JSONObject watchOverview(HttpSession session, JSONObject json) {
Long overviewId = json.getLong("overviewId");
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
ProjectOverview overview = requestManager.getProjectOverviewById(overviewId);
if (!overview.getWatchers().contains(user)) {
watchManager.watch(overview, user);
watchManager.watch(overview.getProject(), user);
requestManager.saveProjectOverview(overview);
requestManager.saveProject(overview.getProject());
}
return JSONUtils.SimpleJSONResponse("OK");
}
catch (IOException e) {
e.printStackTrace();
}
return JSONUtils.SimpleJSONError("Unable to watch/unwatch overview");
}
public JSONObject unwatchOverview(HttpSession session, JSONObject json) {
Long overviewId = json.getLong("overviewId");
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
ProjectOverview overview = requestManager.getProjectOverviewById(overviewId);
if (!overview.getProject().getSecurityProfile().getOwner().equals(user)) {
if (overview.getWatchers().contains(user)) {
watchManager.unwatch(overview, user);
watchManager.unwatch(overview.getProject(), user);
requestManager.saveProjectOverview(overview);
requestManager.saveProject(overview.getProject());
}
return JSONUtils.SimpleJSONResponse("OK");
}
else {
return JSONUtils.SimpleJSONError("Cannot unwatch an entity of which you are the owner.");
}
}
catch (IOException e) {
e.printStackTrace();
}
return JSONUtils.SimpleJSONError("Unable to watch/unwatch overview");
}
public JSONObject listWatchOverview(HttpSession session, JSONObject json) {
Long overviewId = json.getLong("overviewId");
StringBuilder sb = new StringBuilder();
JSONObject j = new JSONObject();
try {
User user = securityManager.getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName());
ProjectOverview overview = requestManager.getProjectOverviewById(overviewId);
sb.append("<ul class='bullets' style='margin-left: -30px;'>");
for (User theUser : overview.getWatchers()) {
sb.append("<li>");
sb.append(theUser.getFullName());
sb.append("</li>");
}
sb.append("</ul>");
j.put("watchers", sb.toString());
return j;
}
catch (IOException e) {
e.printStackTrace();
}
return JSONUtils.SimpleJSONError("Unable to list watchers");
}
public JSONObject listSamplesByProject(HttpSession session, JSONObject json) {
Long projectId = json.getLong("projectId");
try {
JSONObject j = new JSONObject();
JSONArray jsonArray = new JSONArray();
for (Sample sample : requestManager.listAllSamplesByProjectId(projectId)) {
jsonArray.add("{'id':'" + sample.getId() + "'," +
"'name':'" + sample.getName() + "'," +
"'alias':'"+sample.getAlias() + "'," +
"'type':'"+sample.getSampleType() + "'," +
"'description':'"+sample.getDescription() + "'}");
}
j.put("array", jsonArray);
return j;
}
catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
}
public JSONObject addSampleGroup(HttpSession session, JSONObject json) {
Long overviewId = json.getLong("overviewId");
try {
ProjectOverview overview = requestManager.getProjectOverviewById(overviewId);
Set<Sample> samples = new HashSet<>();
if (json.has("samples")) {
JSONArray a = JSONArray.fromObject(json.get("samples"));
for (JSONObject j : (Iterable<JSONObject>) a) {
if (j.has("sampleId")) {
samples.add(requestManager.getSampleById(j.getLong("sampleId")));
}
else {
return JSONUtils.SimpleJSONError("Unable to add Sample Group: invalid sample set JSON has missing sampleId");
}
}
}
EntityGroup<ProjectOverview, Sample> osg = new EntityGroupImpl<>();
osg.setEntities(samples);
osg.setParent(overview);
overview.setSampleGroup(osg);
requestManager.saveProjectOverview(overview);
requestManager.saveProject(overview.getProject());
return JSONUtils.SimpleJSONResponse("OK");
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Unable to add Sample Group: " + e.getMessage());
}
}
public JSONObject addSamplesToGroup(HttpSession session, JSONObject json) {
Long overviewId = json.getLong("overviewId");
Long groupId = json.getLong("groupId");
try {
ProjectOverview overview = requestManager.getProjectOverviewById(overviewId);
EntityGroup<ProjectOverview, Sample> osg = overview.getSampleGroup();
if (osg != null && groupId != null && osg.getId() == groupId.longValue()) {
if (json.has("samples")) {
JSONArray a = JSONArray.fromObject(json.get("samples"));
for (JSONObject j : (Iterable<JSONObject>) a) {
if (j.has("sampleId")) {
Sample s = requestManager.getSampleById(j.getLong("sampleId"));
if (osg.getEntities().contains(s)) {
log.error("Sample group already contains " + s.getName());
}
else {
osg.addEntity(s);
}
}
else {
return JSONUtils.SimpleJSONError("Unable to add Sample Group: invalid sample set JSON has missing sampleId");
}
}
}
}
requestManager.saveProjectOverview(overview);
requestManager.saveProject(overview.getProject());
return JSONUtils.SimpleJSONResponse("OK");
}
catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Unable to add Sample Group: " + e.getMessage());
}
}
}