Java tutorial
/* * 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.User; import com.eaglegenomics.simlims.core.manager.SecurityManager; import net.sf.json.JSONArray; import net.sf.json.JSONObject; import net.sourceforge.fluxion.ajax.Ajaxified; import net.sourceforge.fluxion.ajax.util.JSONUtils; import org.apache.commons.codec.binary.Base64; 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 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.emPCRDilution; 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.MalformedExperimentException; 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.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.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.*; /** * uk.ac.bbsrc.tgac.miso.spring.ajax * <p/> * Info * * @author Rob Davey * @since 0.0.2 */ @Ajaxified public class PoolControllerHelperService { protected static final Logger log = LoggerFactory.getLogger(PoolControllerHelperService.class); @Autowired private SecurityManager securityManager; @Autowired private RequestManager requestManager; @Autowired private DataObjectFactory dataObjectFactory; @Autowired private MisoFilesManager misoFileManager; @Autowired private BarcodeFactory barcodeFactory; @Autowired private PrintManager<MisoPrintService, Queue<?>> printManager; public JSONObject getPoolQcTypes(HttpSession session, JSONObject json) { try { StringBuilder sb = new StringBuilder(); Collection<QcType> types = requestManager.listAllPoolQcTypes(); 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 Pool QC Types"); } public JSONObject addPoolQC(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("poolId") && !json.get("poolId").equals("")) { Long poolId = Long.parseLong(json.getString("poolId")); Pool<? extends Poolable> pool = requestManager.getPoolById(poolId); PoolQC newQc = dataObjectFactory.getPoolQC(); if (json.has("qcPassed") && json.getString("qcPassed").equals("true")) { pool.setQcPassed(true); } newQc.setQcCreator(json.getString("qcCreator")); newQc.setQcDate(new SimpleDateFormat("dd/MM/yyyy").parse(json.getString("qcDate"))); newQc.setQcType(requestManager.getPoolQcTypeById(json.getLong("qcType"))); newQc.setResults(Double.parseDouble(json.getString("results"))); pool.addQc(newQc); requestManager.savePoolQC(newQc); StringBuilder sb = new StringBuilder(); sb.append("<tr><th>QCed By</th><th>QC Date</th><th>Method</th><th>Results</th></tr>"); for (PoolQC qc : pool.getPoolQCs()) { sb.append("<tr>"); 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("</tr>"); } return JSONUtils.SimpleJSONResponse(sb.toString()); } else { return JSONUtils.SimpleJSONError("Cannot detect parent pool ID. Cannot add PoolQC"); } } catch (Exception e) { log.error("Failed to add Pool QC to this Pool: ", e); return JSONUtils.SimpleJSONError("Failed to add Pool QC to this Pool: " + e.getMessage()); } } public JSONObject bulkAddPoolQCs(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"); if (qcPassed == null || qcPassed.equals("") || qcType == null || qcType.equals("") || results == null || results.equals("") || qcCreator == null || qcCreator.equals("") || qcDate == null || qcDate.equals("")) { ok = false; } } //persist if (ok) { Map<String, Object> map = new HashMap<String, Object>(); JSONArray a = new JSONArray(); for (JSONObject qc : (Iterable<JSONObject>) qcs) { JSONObject j = addPoolQC(session, qc); j.put("poolId", qc.getString("poolId")); a.add(j); } map.put("saved", a); return JSONUtils.JSONObjectResponse(map); } else { log.error( "Failed to add Pool QC to this Pool: one of the required fields of the selected QCs is missing or invalid"); return JSONUtils.SimpleJSONError( "Failed to add Pool QC to this Pool: one of the required fields of the selected QCs is missing or invalid"); } } catch (Exception e) { log.error("Failed to add Pool QC to this Pool: ", e); return JSONUtils.SimpleJSONError("Failed to add Pool QC to this Pool: " + e.getMessage()); } } public JSONObject changePoolQCRow(HttpSession session, JSONObject json) { try { JSONObject response = new JSONObject(); Long qcId = Long.parseLong(json.getString("qcId")); PoolQC poolQc = requestManager.getPoolQCById(qcId); response.put("results", "<input type='text' id='" + qcId + "' value='" + poolQc.getResults() + "'/>"); response.put("edit", "<a href='javascript:void(0);' onclick='Pool.qc.editPoolQC(\"" + qcId + "\");'>Save</a>"); return response; } catch (Exception e) { log.error("Failed to display Pool QC of this sample: ", e); return JSONUtils.SimpleJSONError("Failed to display Pool QC of this sample: " + e.getMessage()); } } public JSONObject editPoolQC(HttpSession session, JSONObject json) { try { if (json.has("qcId") && !json.get("qcId").equals("")) { Long qcId = Long.parseLong(json.getString("qcId")); PoolQC poolQc = requestManager.getPoolQCById(qcId); poolQc.setResults(Double.parseDouble(json.getString("result"))); requestManager.savePoolQC(poolQc); return JSONUtils.SimpleJSONResponse("OK"); } } catch (Exception e) { log.error("Failed to add Pool QC to this sample: ", e); return JSONUtils.SimpleJSONError("Failed to add Pool QC to this sample: " + e.getMessage()); } return JSONUtils.SimpleJSONError("Cannot add PoolQC"); } private String processDilutions(Set<String> codes) throws IOException { StringBuilder sb = new StringBuilder(); sb.append("<div id='dilslist' class='checklist' style='width: 100%;'>"); for (String s : codes) { if (LimsUtils.isBase64String(s)) { //Base64-encoded string, most likely a barcode image beeped in. decode and search s = new String(Base64.decodeBase64(s)); } Dilution ed = requestManager.getDilutionByBarcode(s); if (ed != null) { sb.append("<span>"); sb.append("<input type='checkbox' value='" + s + "' name='importdilslist' id='importdilslist_" + ed.getName() + "'/>"); sb.append("<label for='importdilslist_" + ed.getName() + "'>" + ed.getName() + " (" + s + ")</label>"); sb.append("</span>"); } } sb.append("</div>"); sb.append( "<a onclick='Utils.ui.checkAll(\"importdilslist\"); return false;' href='javascript:void(0);'>All</a> " + "/ <a onclick='Utils.ui.uncheckAll(\"importdilslist\"); return false;' href='javascript:void(0);'>None</a>"); sb.append("<br/><button type='submit' class='br-button ui-state-default ui-corner-all'>Use</button>"); return sb.toString(); } @Deprecated private String processLibraryDilutions(Set<String> codes) throws IOException { StringBuilder sb = new StringBuilder(); sb.append("<div id='dilslist' class='checklist' style='width: 100%;'>"); for (String s : codes) { if (LimsUtils.isBase64String(s)) { //Base64-encoded string, most likely a barcode image beeped in. decode and search s = new String(Base64.decodeBase64(s)); } LibraryDilution ed = requestManager.getLibraryDilutionByBarcode(s); if (ed != null) { sb.append("<span>"); sb.append("<input type='checkbox' value='" + s + "' name='importdilslist' id='importdilslist_" + ed.getName() + "'/>"); sb.append("<label for='importdilslist_" + ed.getName() + "'>" + ed.getName() + " (" + s + ")</label>"); sb.append("</span>"); } } sb.append("</div>"); sb.append( "<a onclick='Utils.ui.checkAll(\"importdilslist\"); return false;' href='javascript:void(0);'>All</a> " + "/ <a onclick='Utils.ui.uncheckAll(\"importdilslist\"); return false;' href='javascript:void(0);'>None</a>"); sb.append("<br/><button type='submit' class='br-button ui-state-default ui-corner-all'>Use</button>"); return sb.toString(); } @Deprecated private String processEmPcrDilutions(Set<String> codes) throws IOException { StringBuilder sb = new StringBuilder(); sb.append("<div id='dilslist' class='checklist' style='width: 100%;'>"); for (String s : codes) { if (LimsUtils.isBase64String(s)) { //Base64-encoded string, most likely a barcode image beeped in. decode and search s = new String(Base64.decodeBase64(s)); } emPCRDilution ed = requestManager.getEmPcrDilutionByBarcode(s); if (ed != null) { sb.append("<span>"); sb.append("<input type='checkbox' value='" + s + "' name='importdilslist' id='importdilslist_" + ed.getName() + "'/>"); sb.append("<label for='importdilslist_" + ed.getName() + "'>" + ed.getName() + " (" + s + ")</label>"); sb.append("</span>"); } } sb.append("</div>"); sb.append( "<a onclick='Utils.ui.checkAll(\"importdilslist\"); return false;' href='javascript:void(0);'>All</a> " + "/ <a onclick='Utils.ui.uncheckAll(\"importdilslist\"); return false;' href='javascript:void(0);'>None</a>"); sb.append("<br/><button type='submit' class='br-button ui-state-default ui-corner-all'>Use</button>"); return sb.toString(); } @Deprecated public JSONObject selectLibraryDilutionsByBarcodeList(HttpSession session, JSONObject json) { try { if (json.has("barcodes")) { String barcodes = json.getString("barcodes"); String[] codes = barcodes.split("\n"); // make sure there are no duplicates and order the strings // by putitng the codes in a treeset TreeSet<String> hcodes = new TreeSet<String>(); hcodes.addAll(Arrays.asList(codes)); StringBuilder sb = new StringBuilder(); sb.append("<form action='/miso/pool/illumina/import' method='post'>"); sb.append("<div style='width: 100%;'>"); sb.append(processLibraryDilutions(hcodes)); sb.append("</form>"); sb.append("</div>"); session.removeAttribute("barcodes"); return JSONUtils.SimpleJSONResponse(sb.toString()); } } catch (Exception e) { log.debug("Failed to generate barcode selection: ", e); return JSONUtils.SimpleJSONError("Failed to generate barcode selection"); } return JSONUtils.SimpleJSONError("Cannot select barcodes"); } public JSONObject selectDilutionsByBarcodeFile(HttpSession session, JSONObject json) { try { JSONObject barcodes = (JSONObject) session.getAttribute("barcodes"); log.debug(barcodes.toString()); if (barcodes.has("barcodes")) { JSONArray a = barcodes.getJSONArray("barcodes"); // make sure there are no duplicates and order the strings // by putitng the codes in a treeset TreeSet<String> hcodes = new TreeSet<String>(); hcodes.addAll(Arrays.asList((String[]) a.toArray(new String[0]))); StringBuilder sb = new StringBuilder(); sb.append("<form action='/miso/pool/import' method='post'>"); sb.append("<div style='width: 100%;'>"); sb.append(processDilutions(hcodes)); sb.append("</form>"); sb.append("</div>"); session.removeAttribute("barcodes"); return JSONUtils.SimpleJSONResponse(sb.toString()); } } catch (Exception e) { log.debug("Failed to generate barcode selection: ", e); return JSONUtils.SimpleJSONError("Failed to generate barcode selection"); } return JSONUtils.SimpleJSONError("Cannot select barcodes"); } public JSONObject selectDilutionsByBarcodeList(HttpSession session, JSONObject json) { try { if (json.has("barcodes")) { String barcodes = json.getString("barcodes"); String[] codes = barcodes.split("\n"); // make sure there are no duplicates and order the strings // by putitng the codes in a treeset TreeSet<String> hcodes = new TreeSet<String>(); hcodes.addAll(Arrays.asList(codes)); StringBuilder sb = new StringBuilder(); sb.append("<form action='/miso/pool/import' method='post'>"); sb.append("<div style='width: 100%;'>"); sb.append(processDilutions(hcodes)); sb.append("</form>"); sb.append("</div>"); session.removeAttribute("barcodes"); return JSONUtils.SimpleJSONResponse(sb.toString()); } } catch (Exception e) { log.debug("Failed to generate barcode selection: ", e); return JSONUtils.SimpleJSONError("Failed to generate barcode selection"); } return JSONUtils.SimpleJSONError("Cannot select barcodes"); } @Deprecated public JSONObject selectLibraryDilutionsByBarcodeFile(HttpSession session, JSONObject json) { try { JSONObject barcodes = (JSONObject) session.getAttribute("barcodes"); log.debug(barcodes.toString()); if (barcodes.has("barcodes")) { JSONArray a = barcodes.getJSONArray("barcodes"); // make sure there are no duplicates and order the strings // by putitng the codes in a treeset TreeSet<String> hcodes = new TreeSet<String>(); hcodes.addAll(Arrays.asList((String[]) a.toArray(new String[0]))); StringBuilder sb = new StringBuilder(); sb.append("<form action='/miso/pool/import' method='post'>"); sb.append("<div style='width: 100%;'>"); sb.append(processLibraryDilutions(hcodes)); sb.append("</form>"); sb.append("</div>"); session.removeAttribute("barcodes"); return JSONUtils.SimpleJSONResponse(sb.toString()); } } catch (Exception e) { log.debug("Failed to generate barcode selection: ", e); return JSONUtils.SimpleJSONError("Failed to generate barcode selection"); } return JSONUtils.SimpleJSONError("Cannot select barcodes"); } @Deprecated public JSONObject select454EmPCRDilutionsByBarcodeList(HttpSession session, JSONObject json) { try { if (json.has("barcodes")) { String barcodes = json.getString("barcodes"); String[] codes = barcodes.split("\n"); // make sure there are no duplicates and order the strings // by putitng the codes in a treeset TreeSet<String> hcodes = new TreeSet<String>(); hcodes.addAll(Arrays.asList(codes)); StringBuilder sb = new StringBuilder(); sb.append("<div style='width: 100%;'>"); sb.append("<form action='/miso/pool/ls454/import' method='post'>"); sb.append(processEmPcrDilutions(hcodes)); sb.append("</form>"); sb.append("</div>"); session.removeAttribute("barcodes"); return JSONUtils.SimpleJSONResponse(sb.toString()); } } catch (Exception e) { log.debug("Failed to generate barcode selection: ", e); return JSONUtils.SimpleJSONError("Failed to generate barcode selection"); } return JSONUtils.SimpleJSONError("Cannot select barcodes"); } @Deprecated public JSONObject select454EmPCRDilutionsByBarcodeFile(HttpSession session, JSONObject json) { try { JSONObject barcodes = (JSONObject) session.getAttribute("barcodes"); log.debug(barcodes.toString()); if (barcodes.has("barcodes")) { JSONArray a = barcodes.getJSONArray("barcodes"); // make sure there are no duplicates and order the strings // by putitng the codes in a treeset TreeSet<String> hcodes = new TreeSet<String>(); hcodes.addAll(Arrays.asList((String[]) a.toArray(new String[0]))); StringBuilder sb = new StringBuilder(); sb.append("<div style='width: 100%;'>"); sb.append("<form action='/miso/pool/ls454/import' method='post'>"); sb.append(processEmPcrDilutions(hcodes)); sb.append("</form>"); sb.append("</div>"); session.removeAttribute("barcodes"); return JSONUtils.SimpleJSONResponse(sb.toString()); } } catch (Exception e) { log.debug("Failed to generate barcode selection: ", e); return JSONUtils.SimpleJSONError("Failed to generate barcode selection"); } return JSONUtils.SimpleJSONError("Cannot select barcodes"); } @Deprecated public JSONObject selectSolidEmPCRDilutionsByBarcodeList(HttpSession session, JSONObject json) { try { if (json.has("barcodes")) { String barcodes = json.getString("barcodes"); String[] codes = barcodes.split("\n"); // make sure there are no duplicates and order the strings // by putitng the codes in a treeset TreeSet<String> hcodes = new TreeSet<String>(); hcodes.addAll(Arrays.asList(codes)); StringBuilder sb = new StringBuilder(); sb.append("<div style='width: 100%;'>"); sb.append("<form action='/miso/pool/solid/import' method='post'>"); sb.append(processEmPcrDilutions(hcodes)); sb.append("</form>"); sb.append("</div>"); session.removeAttribute("barcodes"); return JSONUtils.SimpleJSONResponse(sb.toString()); } } catch (Exception e) { log.debug("Failed to generate barcode selection: ", e); return JSONUtils.SimpleJSONError("Failed to generate barcode selection"); } return JSONUtils.SimpleJSONError("Cannot select barcodes"); } @Deprecated public JSONObject selectSolidEmPCRDilutionsByBarcodeFile(HttpSession session, JSONObject json) { try { JSONObject barcodes = (JSONObject) session.getAttribute("barcodes"); log.debug(barcodes.toString()); if (barcodes.has("barcodes")) { JSONArray a = barcodes.getJSONArray("barcodes"); // make sure there are no duplicates and order the strings // by putitng the codes in a treeset TreeSet<String> hcodes = new TreeSet<String>(); hcodes.addAll(Arrays.asList((String[]) a.toArray(new String[0]))); StringBuilder sb = new StringBuilder(); sb.append("<div style='width: 100%;'>"); sb.append("<form action='/miso/pool/solid/import' method='post'>"); sb.append(processEmPcrDilutions(hcodes)); sb.append("</form>"); sb.append("</div>"); session.removeAttribute("barcodes"); return JSONUtils.SimpleJSONResponse(sb.toString()); } } catch (Exception e) { log.debug("Failed to generate barcode selection: ", e); return JSONUtils.SimpleJSONError("Failed to generate barcode selection"); } return JSONUtils.SimpleJSONError("Cannot select barcodes"); } public JSONObject getPoolBarcode(HttpSession session, JSONObject json) { Long poolId = json.getLong("poolId"); File temploc = new File(session.getServletContext().getRealPath("/") + "temp/"); try { Pool pool = requestManager.getPoolById(poolId); 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(pool, bg, dim); } else { return JSONUtils.SimpleJSONError( "'" + json.getString("barcodeGenerator") + "' is not a valid barcode generator type"); } } else { bi = barcodeFactory.generateSquareDataMatrix(pool, 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("Pool has no parseable barcode"); } } catch (IOException e) { e.printStackTrace(); return JSONUtils .SimpleJSONError(e.getMessage() + ": Cannot seem to access " + temploc.getAbsolutePath()); } } public JSONObject printPoolBarcodes(HttpSession session, JSONObject json) { try { User user = securityManager .getUserByLoginName(SecurityContextHolder.getContext().getAuthentication().getName()); JSONArray ss = JSONArray.fromObject(json.getString("pools")); 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(Pool.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) { try { Long poolId = p.getLong("poolId"); Pool pool = requestManager.getPoolById(poolId); File f = mps.getLabelFor(pool); if (f != null) thingsToPrint.add(f); } catch (IOException e) { e.printStackTrace(); return JSONUtils.SimpleJSONError("Error printing pool barcode: " + 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("No printer of that name available: " + e.getMessage()); } catch (IOException e) { e.printStackTrace(); return JSONUtils.SimpleJSONError("Cannot print barcodes: " + e.getMessage()); } } public JSONObject poolSearchExperiments(HttpSession session, JSONObject json) { String searchStr = json.getString("str"); String platformType = json.getString("platform").toUpperCase(); try { if (searchStr.length() > 1) { String str = searchStr.toLowerCase(); StringBuilder b = new StringBuilder(); List<Experiment> experiments = new ArrayList<Experiment>(requestManager.listAllExperiments()); int numMatches = 0; for (Experiment e : experiments) { if (e.getPlatform().getPlatformType().equals(PlatformType.valueOf(platformType))) { String expName = e.getName() == null ? null : e.getName(); if (expName != null && (expName.toLowerCase().equals(str) || expName.toLowerCase().contains(str)) || (e.getStudy().getAlias().toLowerCase().contains(str) || e.getStudy().getName().toLowerCase().contains(str)) || (e.getStudy().getProject().getAlias().toLowerCase().contains(str) || e.getStudy().getProject().getName().toLowerCase().contains(str))) { b.append( "<div onmouseover=\"this.className='autocompleteboxhighlight'\" onmouseout=\"this.className='autocompletebox'\" class=\"autocompletebox\"" + " onclick=\"Pool.search.poolSearchSelectExperiment('" + e.getId() + "', '" + e.getName() + "')\">" + "<b>Experiment:</b> " + expName + "<br/>" + "<b>Description:</b> " + e.getDescription() + "<br/>" + "<b>Project:</b> " + e.getStudy().getProject().getAlias() + "<br/>" + "</div>"); numMatches++; } } } if (numMatches == 0) { return JSONUtils.JSONObjectResponse("html", "No matches"); } else { return JSONUtils.JSONObjectResponse("html", "<div class=\"autocomplete\"><ul>" + b.toString() + "</ul></div>"); } } else { return JSONUtils.JSONObjectResponse("html", "Need a longer search pattern ..."); } } catch (Exception e) { e.printStackTrace(); return JSONUtils.SimpleJSONError(e.getMessage()); } } @Deprecated public JSONObject poolSearchDilution(HttpSession session, JSONObject json) { String searchStr = json.getString("str"); String platformType = json.getString("platform").toUpperCase(); try { if (searchStr.length() > 1) { if (LimsUtils.isBase64String(searchStr)) { //Base64-encoded string, most likely a barcode image beeped in. decode and search searchStr = new String(Base64.decodeBase64(searchStr)); } //String str = searchStr.toLowerCase(); StringBuilder b = new StringBuilder(); List<? extends Dilution> dilutions = new ArrayList<Dilution>( requestManager.listDilutionsBySearch(searchStr, PlatformType.valueOf(platformType))); int numMatches = 0; for (Dilution d : dilutions) { b.append( "<div onmouseover=\"this.className='autocompleteboxhighlight'\" onmouseout=\"this.className='autocompletebox'\" class=\"autocompletebox\"" + " onclick=\"Pool.search.poolSearchSelectDilution('" + d.getId() + "', '" + d.getName() + "')\">" + "<b>Dilution: " + d.getName() + "</b><br/>" + "<b>Library: " + d.getLibrary().getAlias() + "</b><br/>" + "<b>Sample: " + d.getLibrary().getSample().getAlias() + "</b><br/>" + "</div>"); numMatches++; } if (numMatches == 0) { return JSONUtils.JSONObjectResponse("html", "No matches"); } else { return JSONUtils.JSONObjectResponse("html", "<div class=\"autocomplete\"><ul>" + b.toString() + "</ul></div>"); } } else { return JSONUtils.JSONObjectResponse("html", "Need a longer search pattern ..."); } } catch (Exception e) { e.printStackTrace(); return JSONUtils.SimpleJSONError(e.getMessage()); } } @Deprecated public JSONObject poolSearchLibraryDilution(HttpSession session, JSONObject json) { String searchStr = json.getString("str"); String platformType = json.getString("platform").toUpperCase(); try { if (searchStr.length() > 1) { if (LimsUtils.isBase64String(searchStr)) { //Base64-encoded string, most likely a barcode image beeped in. decode and search searchStr = new String(Base64.decodeBase64(searchStr)); } //String str = searchStr.toLowerCase(); StringBuilder b = new StringBuilder(); List<LibraryDilution> dilutions = new ArrayList<LibraryDilution>(requestManager .listAllLibraryDilutionsBySearch(searchStr, PlatformType.valueOf(platformType))); int numMatches = 0; for (LibraryDilution d : dilutions) { /* String dilName = d.getName() == null ? null : d.getName(); if (dilName != null && (dilName.toLowerCase().equals(str) || dilName.toLowerCase().contains(str)) || (d.getLibrary().getAlias().toLowerCase().contains(str) || d.getLibrary().getName().toLowerCase().contains(str)) || (d.getLibrary().getSample().getAlias().toLowerCase().contains(str) || d.getLibrary().getSample().getName().toLowerCase().contains(str))) { */ b.append( "<div onmouseover=\"this.className='autocompleteboxhighlight'\" onmouseout=\"this.className='autocompletebox'\" class=\"autocompletebox\"" + " onclick=\"Pool.search.poolSearchSelectDilution('" + d.getId() + "', '" + d.getName() + "')\">" + "<b>Dilution: " + d.getName() + "</b><br/>" + "<b>Library: " + d.getLibrary().getAlias() + "</b><br/>" + "<b>Sample: " + d.getLibrary().getSample().getAlias() + "</b><br/>" + "</div>"); numMatches++; //} } if (numMatches == 0) { return JSONUtils.JSONObjectResponse("html", "No matches"); } else { return JSONUtils.JSONObjectResponse("html", "<div class=\"autocomplete\"><ul>" + b.toString() + "</ul></div>"); } } else { return JSONUtils.JSONObjectResponse("html", "Need a longer search pattern ..."); } } catch (Exception e) { e.printStackTrace(); return JSONUtils.SimpleJSONError(e.getMessage()); } } @Deprecated public JSONObject poolSearchEmPcrDilution(HttpSession session, JSONObject json) { String searchStr = json.getString("str"); String platformType = json.getString("platform").toUpperCase(); try { if (searchStr.length() > 1) { if (LimsUtils.isBase64String(searchStr)) { //Base64-encoded string, most likely a barcode image beeped in. decode and search searchStr = new String(Base64.decodeBase64(searchStr)); } //String str = searchStr.toLowerCase(); StringBuilder b = new StringBuilder(); List<emPCRDilution> dilutions = new ArrayList<emPCRDilution>(requestManager .listAllEmPcrDilutionsBySearch(searchStr, PlatformType.valueOf(platformType))); int numMatches = 0; for (emPCRDilution d : dilutions) { /* String dilName = d.getName() == null ? null : d.getName(); if (dilName != null && (dilName.toLowerCase().equals(str) || dilName.toLowerCase().contains(str)) || (d.getLibrary().getAlias().toLowerCase().contains(str) || d.getLibrary().getName().toLowerCase().contains(str)) || (d.getLibrary().getSample().getAlias().toLowerCase().contains(str) || d.getLibrary().getSample().getName().toLowerCase().contains(str))) { */ b.append( "<div onmouseover=\"this.className='autocompleteboxhighlight'\" onmouseout=\"this.className='autocompletebox'\" class=\"autocompletebox\"" + " onclick=\"Pool.search.poolSearchSelectDilution('" + d.getId() + "', '" + d.getName() + "')\">" + "<b>Dilution: " + d.getName() + "</b><br/>" + "<b>Library: " + d.getLibrary().getAlias() + "</b><br/>" + "<b>Sample: " + d.getLibrary().getSample().getAlias() + "</b><br/>" + "</div>"); numMatches++; //} } if (numMatches == 0) { return JSONUtils.JSONObjectResponse("html", "No matches"); } else { return JSONUtils.JSONObjectResponse("html", "<div class=\"autocomplete\"><ul>" + b.toString() + "</ul></div>"); } } else { return JSONUtils.JSONObjectResponse("html", "Need a longer search pattern ..."); } } catch (Exception e) { e.printStackTrace(); return JSONUtils.SimpleJSONError(e.getMessage()); } } public JSONObject checkPoolExperiment(HttpSession session, JSONObject json) { try { String partition = json.getString("partition"); Long poolId = json.getLong("poolId"); Pool<? extends Poolable> p = requestManager.getPoolById(poolId); StringBuilder sb = new StringBuilder(); if (p.getExperiments().size() == 0) { Set<Project> pooledProjects = new HashSet<Project>(); Collection<? extends Poolable> ds = p.getPoolableElements(); for (Poolable d : ds) { if (d instanceof Dilution) { pooledProjects.add(((Dilution) d).getLibrary().getSample().getProject()); } else if (d instanceof Plate) { Plate plate = (Plate) d; if (!plate.getElements().isEmpty()) { if (plate.getElementType().equals(Library.class)) { Library l = (Library) plate.getElements().get(0); pooledProjects.add(l.getSample().getProject()); } } } } sb.append("<div style='float:left; clear:both'>"); for (Project project : pooledProjects) { sb.append("<div id='studySelectDiv" + partition + "_" + project.getProjectId() + "'>"); sb.append(project.getAlias() + ": <select name='poolStudies" + partition + "_" + project.getProjectId() + "' id='poolStudies" + partition + "_" + project.getProjectId() + "'>"); Collection<Study> studies = requestManager.listAllStudiesByProjectId(project.getProjectId()); if (studies.isEmpty()) { //throw new Exception("No studies available on project " + project.getName() + ". At least one study must be available for each project associated with this Pool."); return JSONUtils.SimpleJSONError("No studies available on project " + project.getName() + ". At least one study must be available for each project associated with this Pool."); } else { for (Study s : studies) { sb.append("<option value='" + s.getId() + "'>" + s.getAlias() + " (" + s.getName() + " - " + s.getStudyType() + ")</option>"); } } sb.append("</select>"); sb.append("<input id='studySelectButton-" + partition + "_" + p.getId() + "' type='button' onclick=\"Run.container.selectStudy('" + partition + "', " + p.getId() + "," + project.getProjectId() + ");\" class=\"ui-state-default ui-corner-all\" value='Select Study'/>"); sb.append("</div><br/>"); } sb.append("</div>"); } return JSONUtils.JSONObjectResponse("html", sb.toString()); } catch (Exception e) { e.printStackTrace(); return JSONUtils.SimpleJSONError(e.getMessage()); } } public JSONObject selectStudyForPool(HttpSession session, JSONObject json) { try { Long poolId = json.getLong("poolId"); Pool p = requestManager.getPoolById(poolId); Long studyId = json.getLong("studyId"); Study s = requestManager.getStudyById(studyId); if (json.has("runId") && json.get("runId") != null) { Long runId = json.getLong("runId"); Run r = requestManager.getRunById(runId); if (r != null) { StringBuilder sb = new StringBuilder(); Experiment e = dataObjectFactory.getExperiment(); e.setAlias("EXP_AUTOGEN_" + s.getName() + "_" + s.getStudyType() + "_" + (s.getExperiments().size() + 1)); e.setTitle(s.getProject().getName() + " " + r.getPlatformType().getKey() + " " + s.getStudyType() + " experiment (Auto-gen)"); e.setDescription(s.getProject().getAlias()); e.setPlatform(r.getSequencerReference().getPlatform()); e.setStudy(s); e.setSecurityProfile(s.getSecurityProfile()); try { p.addExperiment(e); requestManager.saveExperiment(e); } catch (MalformedExperimentException e1) { e1.printStackTrace(); } sb.append("<i>"); sb.append("<span>" + s.getProject().getAlias() + " (" + e.getName() + ": " + p.getDilutions().size() + " dilutions)</span><br/>"); sb.append("</i>"); return JSONUtils.JSONObjectResponse("html", sb.toString()); } else { return JSONUtils.SimpleJSONError("Could not find run with ID " + runId); } } else { return JSONUtils.SimpleJSONError( "Could not resolve Run ID. Please ensure the run is saved before adding Pools"); } } catch (Exception e) { e.printStackTrace(); return JSONUtils.SimpleJSONError(e.getMessage()); } } public JSONObject listPoolAverageInsertSizes(HttpSession session, JSONObject json) { try { JSONObject j = new JSONObject(); for (Pool<? extends Poolable> pool : requestManager.listAllPools()) { StringBuilder b = new StringBuilder(); Collection<? extends Dilution> dls = pool.getDilutions(); if (dls.size() > 0) { int sum = 0; int count = 0; for (Dilution ld : dls) { List<LibraryQC> libraryQCs = new ArrayList<LibraryQC>( requestManager.listAllLibraryQCsByLibraryId(ld.getLibrary().getId())); if (libraryQCs.size() > 0) { //List<LibraryQC> libraryQCsList = new ArrayList<LibraryQC>(libraryQCs); //Collections.sort(libraryQCsList); LibraryQC libraryQC = libraryQCs.get(libraryQCs.size() - 1); sum += libraryQC.getInsertSize(); count++; } } if (count > 0) { b.append(Math.round(sum / count) + " bp"); } } else { b.append("No QC"); } j.put(pool.getId(), b.toString()); } return j; } catch (IOException e) { log.debug("Failed", e); return JSONUtils.SimpleJSONError(e.getMessage()); } } public JSONObject checkAverageInsertSizeByPoolId(HttpSession session, JSONObject json) { try { JSONObject j = new JSONObject(); Long poolId = json.getLong("poolId"); Pool pool = requestManager.getPoolById(poolId); StringBuilder b = new StringBuilder(); Collection<? extends Dilution> dls = pool.getDilutions(); if (dls.size() > 0) { int sum = 0; int count = 0; for (Dilution ld : dls) { List<LibraryQC> libraryQCs = new ArrayList<LibraryQC>( requestManager.listAllLibraryQCsByLibraryId(ld.getLibrary().getId())); if (libraryQCs.size() > 0) { LibraryQC libraryQC = libraryQCs.get(libraryQCs.size() - 1); sum += libraryQC.getInsertSize(); count++; } } if (count > 0) { b.append(Math.round(sum / count) + " bp"); } } else { b.append("No QC"); } j.put("response", b.toString()); return j; } catch (IOException e) { log.debug("Failed", e); return JSONUtils.SimpleJSONError(e.getMessage()); } } public JSONObject checkConcentrationByPoolId(HttpSession session, JSONObject json) { try { JSONObject j = new JSONObject(); Long poolId = json.getLong("poolId"); Pool pool = requestManager.getPoolById(poolId); double concentration = pool.getConcentration(); j.put("response", concentration); return j; } catch (IOException e) { log.debug("Failed", e); return JSONUtils.SimpleJSONError(e.getMessage()); } } public JSONObject checkInfoByPoolId(HttpSession session, JSONObject json) { try { JSONObject j = new JSONObject(); Long poolId = json.getLong("poolId"); Pool<? extends Poolable> pool = requestManager.getPoolById(poolId); StringBuilder info = new StringBuilder(); if (pool.getDilutions().size() > 0) { info.append("<ul class=\"shorterbullets\">"); Collection<? extends Dilution> dls = pool.getDilutions(); for (Dilution dilution : dls) { info.append("<li><b>" + dilution.getName() + "</b>"); info.append( "<br/><small><u>" + dilution.getLibrary().getSample().getProject().getAlias() + "</u>"); info.append("<br/>" + dilution.getLibrary().getAlias() + " (" + dilution.getLibrary().getName() + ")"); info.append("<br/>" + dilution.getLibrary().getDescription() + " (" + dilution.getLibrary().getSample().getName() + ")</small>"); info.append("</li>"); } info.append("</ul>"); } else if (pool.getPoolableElements().size() > 0) { info.append("<ul class=\"shorterbullets\">"); Collection<? extends Poolable> ds = pool.getPoolableElements(); for (Poolable p : ds) { if (p instanceof Dilution) { Dilution dilution = (Dilution) p; info.append("<li><b>" + dilution.getName() + "</b>"); info.append("<br/><small><u>" + dilution.getLibrary().getSample().getProject().getAlias() + "</u>"); info.append("<br/>" + dilution.getLibrary().getAlias() + " (" + dilution.getLibrary().getName() + ")"); info.append("<br/>" + dilution.getLibrary().getDescription() + " (" + dilution.getLibrary().getSample().getName() + ")</small>"); info.append("</li>"); } else if (p instanceof Plate) { Plate<LinkedList<Plateable>, Plateable> plate = (Plate<LinkedList<Plateable>, Plateable>) p; info.append("<li><b>" + plate.getName() + "</b> [" + plate.getSize() + "-well]"); if (!plate.getElements().isEmpty()) { info.append("<br/><small><u>" + plate.getSize() + "-well " + plate.getElementType().getSimpleName() + " plate</u>"); Plateable element = plate.getElements().getFirst(); if (element instanceof Library) { Library l = (Library) element; info.append("<br/><small><u>" + l.getSample().getProject().getAlias() + " (" + l.getSample().getProject().getName() + ")</u>"); info.append("<br/>Platform: " + l.getPlatformName()); info.append("<br/>Type: " + l.getLibraryType().getDescription()); info.append("<br/>Selection: " + l.getLibrarySelectionType().getName()); info.append("<br/>Strategy: " + l.getLibraryStrategyType().getName()); } else if (element instanceof Dilution) { Dilution l = (Dilution) element; info.append("<br/><small><u>" + l.getLibrary().getSample().getProject().getAlias() + " (" + l.getLibrary().getSample().getProject().getName() + ")</u>"); info.append("<br/>Platform: " + l.getLibrary().getPlatformName()); info.append("<br/>Type: " + l.getLibrary().getLibraryType().getDescription()); info.append( "<br/>Selection: " + l.getLibrary().getLibrarySelectionType().getName()); info.append("<br/>Strategy: " + l.getLibrary().getLibraryStrategyType().getName()); } else if (element instanceof Sample) { Sample l = (Sample) element; info.append("<br/><small><u>" + l.getProject().getAlias() + " (" + l.getProject().getName() + ")</u>"); } } info.append("</li>"); } else { info.append("<li><b>" + p.getName() + "</b>"); } } info.append("</ul>"); } else { info.append("No pooled elements"); } j.put("response", info.toString()); return j; } catch (IOException e) { log.debug("Failed", e); return JSONUtils.SimpleJSONError(e.getMessage()); } } public JSONObject deletePool(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("poolId")) { Long poolId = json.getLong("poolId"); try { requestManager.deletePool(requestManager.getPoolById(poolId)); return JSONUtils.SimpleJSONResponse("Pool deleted"); } catch (IOException e) { e.printStackTrace(); return JSONUtils.SimpleJSONError("Cannot delete pool: " + e.getMessage()); } } else { return JSONUtils.SimpleJSONError("No pool specified to delete."); } } else { return JSONUtils.SimpleJSONError("Only logged-in admins can delete objects."); } } public JSONObject listPoolsDataTable(HttpSession session, JSONObject json) { if (json.has("platform") && !"".equals(json.getString("platform"))) { try { String platform = json.getString("platform"); JSONObject j = new JSONObject(); JSONArray arr = new JSONArray(); for (Pool pool : requestManager.listAllPoolsByPlatform(PlatformType.get(platform))) { JSONArray pout = new JSONArray(); pout.add(pool.getName()); pout.add(pool.getAlias() != null ? pool.getAlias() : ""); pout.add(pool.getCreationDate() != null ? pool.getCreationDate().toString() : ""); pout.add(pool.getId()); pout.add(pool.getId()); pout.add(pool.getId()); pout.add("<a href=\"/miso/pool/" + pool.getId() + "\"><span class=\"ui-icon ui-icon-pencil\"></span></a>"); arr.add(pout); } j.put("pools", arr); return j; } catch (IOException e) { log.debug("Failed", e); return JSONUtils.SimpleJSONError("Failed: " + e.getMessage()); } } else { return JSONUtils.SimpleJSONError("No platform specified"); } } public JSONObject getPoolableElementInfo(HttpSession session, JSONObject json) { if (json.has("poolId") && json.has("elementId")) { try { Long poolId = json.getLong("poolId"); Long elementId = json.getLong("elementId"); Pool<? extends Poolable> pool = requestManager.getPoolById(poolId); StringBuilder info = new StringBuilder(); for (Poolable p : pool.getPoolableElements()) { if (p.getId() == elementId) { if (p instanceof Plate) { Plate<LinkedList<Plateable>, Plateable> plate = (Plate) p; for (Plateable plateable : plate.getElements()) { if (plateable instanceof Plate) { info.append("<b>Internal Plate:</b> <a href='/miso/plate/" + plate.getId() + "'>" + plate.getName() + "</a><br/>"); } else if (p instanceof Library) { Library library = (Library) plateable; info.append("<b>Library:</b> <a href='/miso/library/" + library.getId() + "'>" + library.getAlias() + "(" + library.getName() + ")</a><br/>"); } } } else if (p instanceof Dilution) { Dilution dilution = (Dilution) p; if (dilution instanceof emPCRDilution) { info.append("<b>emPCR:</b> <a href='/miso/empcr/" + ((emPCRDilution) dilution).getEmPCR().getId() + "'>" + ((emPCRDilution) dilution).getEmPCR().getName() + "<br/>"); } info.append("<b>Library:</b> <a href='/miso/library/" + dilution.getLibrary().getId() + "'>" + dilution.getLibrary().getAlias() + "(" + dilution.getLibrary().getName() + ")</a><br/>"); info.append("<b>Sample:</b> <a href='/miso/sample/" + dilution.getLibrary().getSample().getId() + "'>" + dilution.getLibrary().getSample().getAlias() + "(" + dilution.getLibrary().getSample().getName() + ")</a><br/>"); if (pool.getPoolableElements().size() > 1) { Map<Integer, TagBarcode> barcodes = dilution.getLibrary().getTagBarcodes(); if (!barcodes.isEmpty()) { info.append("<b>Barcodes:</b></br>"); for (Integer key : dilution.getLibrary().getTagBarcodes().keySet()) { info.append(key + ":" + barcodes.get(key).getName() + " (" + barcodes.get(key).getSequence() + ")<br/>"); } info.append( "<span class='counter'><img src='/styles/images/status/green.png' border='0'></span>"); } else { info.append("<b>Barcode:</b>"); info.append("<b>Library:</b> <a href='/miso/library/" + dilution.getLibrary().getId() + "'>Choose tag barcode</a>"); info.append( "<span class='counter'><img src='/styles/images/status/red.png' border='0'></span>"); } } } else { info.append("Unrecognised poolable element: " + p.getClass().getSimpleName()); } break; } } return JSONUtils.JSONObjectResponse("info", info.toString()); } catch (IOException e) { log.debug("Failed", e); return JSONUtils.SimpleJSONError("Failed: " + e.getMessage()); } } else { return JSONUtils.SimpleJSONError("No pool or element ID specified"); } } 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; } }