private Element getRunWells(Session sess) { try { Element irNode = ir.toXMLDocument(null, DetailObject.DATE_OUTPUT_SQL).getRootElement(); for (char row = 'A'; row <= 'H'; row++) { for (int col = 1; col <= 12; col++) { for (int quadrant = 0; quadrant < 3; quadrant = quadrant + 2) { Element wellNode = getWellNode(sess, row, col, quadrant); irNode.addContent(wellNode); } } for (int col = 1; col <= 12; col++) { for (int quadrant = 1; quadrant < 4; quadrant = quadrant + 2) { Element wellNode = getWellNode(sess, row, col, quadrant); irNode.addContent(wellNode); } } } return irNode; } catch (Exception e) { LOG.error("An exception has occurred in CreateRunFile ", e); return null; } }
private Element getWellNode(Session sess, char row, int col, int quadrant) { try { String plateQuery = "SELECT p from Plate as p where p.idInstrumentRun=" + ir.getIdInstrumentRun() + " AND p.quadrant=" + quadrant; Plate plate = (Plate) sess.createQuery(plateQuery).uniqueResult(); Element wellNode = new Element("PlateWell"); if (plate != null) { String wellQuery = "SELECT pw from PlateWell as pw where pw.idPlate=" + plate.getIdPlate() + " AND pw.row='" + row + "' AND pw.col=" + col; PlateWell plateWell = (PlateWell) sess.createQuery(wellQuery).uniqueResult(); if (plateWell != null) { plateWell.excludeMethodFromXML("getPlate"); plateWell.excludeMethodFromXML("getSample"); plateWell.excludeMethodFromXML("getAssay"); plateWell.excludeMethodFromXML("getPrimer"); wellNode = plateWell.toXMLDocument(null, DetailObject.DATE_OUTPUT_SQL).getRootElement(); if (plateWell.getAssay() != null) { wellNode.setAttribute("assay", plateWell.getAssay().getDisplay()); } else if (plateWell.getPrimer() != null) { wellNode.setAttribute("primer", plateWell.getPrimer().getDisplay()); } } else { wellNode.setAttribute("idPlateWell", "0"); } } else { wellNode.setAttribute("idPlateWell", "0"); } return wellNode; } catch (Exception e) { LOG.error("An exception has occurred in CreateRunFile ", e); return null; } }
private void changeRequestsToProcessing(Session sess, InstrumentRun ir) throws ProductException { // Get any requests on that run Map requests = new HashMap(); List wells = sess.createQuery( "SELECT pw from PlateWell as pw " + " join pw.plate as plate where plate.idInstrumentRun =" + ir.getIdInstrumentRun()) .list(); for (Iterator i1 = wells.iterator(); i1.hasNext(); ) { PlateWell well = (PlateWell) i1.next(); if (well.getIdRequest() == null) { break; } if (!well.getIdRequest().equals("") && !requests.containsKey(well.getIdRequest())) { Request req = (Request) sess.get(Request.class, well.getIdRequest()); requests.put(req.getIdRequest(), req); } } // Change request Status for (Iterator i = requests.keySet().iterator(); i.hasNext(); ) { int idReq = (Integer) i.next(); Request req = (Request) sess.get(Request.class, idReq); if (req.getCodeRequestStatus() == null) { ProductUtil.updateLedgerOnRequestStatusChange( sess, req, req.getCodeRequestStatus(), RequestStatus.PROCESSING); req.setCodeRequestStatus(RequestStatus.PROCESSING); } else if (req.getCodeRequestStatus().equals(RequestStatus.NEW) || req.getCodeRequestStatus().equals(RequestStatus.SUBMITTED)) { ProductUtil.updateLedgerOnRequestStatusChange( sess, req, req.getCodeRequestStatus(), RequestStatus.PROCESSING); req.setCodeRequestStatus(RequestStatus.PROCESSING); } } sess.flush(); }
protected void doGet(HttpServletRequest req, HttpServletResponse response) throws ServletException, IOException { // Restrict commands to local host if request is not secure if (!ServletUtil.checkSecureRequest(req, LOG)) { ServletUtil.reportServletError( response, "Secure connection is required. Prefix your request with 'https'", LOG, "Accessing secure command over non-secure line from remote host is not allowed."); return; } // Get the idInstrumentRun if (req.getParameter("idInstrumentRun") != null && !req.getParameter("idInstrumentRun").equals("")) { idInstrumentRun = Integer.valueOf(req.getParameter("idInstrumentRun")); } if (idInstrumentRun == null) { LOG.error("idInstrumentRun required"); response.setContentType("text/html"); response.getOutputStream().println("<html><head><title>Error</title></head>"); response.getOutputStream().println("<body><b>"); response.getOutputStream().println("Missing parameter: idInstrumentRun required" + "<br>"); response.getOutputStream().println("</body>"); response.getOutputStream().println("</html>"); return; } if (req.getParameter("codeReactionType") != null && !req.getParameter("codeReactionType").equals("")) { codeReactionType = req.getParameter("codeReactionType"); } InputStream in = null; SecurityAdvisor secAdvisor = null; try { // Get security advisor secAdvisor = (SecurityAdvisor) req.getSession().getAttribute(SecurityAdvisor.SECURITY_ADVISOR_SESSION_KEY); if (secAdvisor != null) { Session sess = secAdvisor.getHibernateSession( req.getUserPrincipal() != null ? req.getUserPrincipal().getName() : "guest"); ir = (InstrumentRun) sess.load(InstrumentRun.class, idInstrumentRun); String runName = ir.getLabel() != null && !ir.getLabel().equals("") ? ir.getLabel() : ir.getIdInstrumentRun().toString(); runName = runName.replaceAll("\\s", "_"); String runFileName = runName + ".plt"; // Check permissions if (!secAdvisor.hasPermission(SecurityAdvisor.CAN_MANAGE_DNA_SEQ_CORE)) { response.setContentType("text/html"); response.getOutputStream().println("<html><head><title>Error</title></head>"); response.getOutputStream().println("<body><b>"); response .getOutputStream() .println( "DownloadABIRunFileServlet: Insufficient permission to generate ABI Run (.plt) file." + "<br>"); response.getOutputStream().println("</body>"); response.getOutputStream().println("</html>"); System.out.println( "DownloadABIRunFileServlet: Insufficient permission to generate ABI Run (.plt) file."); return; } response.setContentType("application/x-download"); response.setHeader("Content-Disposition", "attachment;filename=" + runFileName); response.setHeader("Cache-Control", "max-age=0, must-revalidate"); OutputStream out = response.getOutputStream(); // Change run status if (ir.getCodeInstrumentRunStatus() == null || ir.getCodeInstrumentRunStatus().equals(InstrumentRunStatus.PENDING)) { ir.setCodeInstrumentRunStatus(InstrumentRunStatus.RUNNING); if (ir.getRunDate() == null) { ir.setRunDate(new java.util.Date(System.currentTimeMillis())); } } changeRequestsToProcessing(sess, ir); sess.flush(); // Run headers if (codeReactionType.equals(ReactionType.FRAGMENT_ANALYSIS_REACTION_TYPE)) { response .getOutputStream() .print( "Container Name\tPlate ID\tDescription\tContainerType\tAppType\tOwner\tOperator\tPlateSealing\tSchedulingPref\t\n"); } else { response .getOutputStream() .print( "Container Name\tPlate ID\tDescription\tApplication\tContainerType\tOwner\tOperator\tPlateSealing\tSchedulingPref\t\r\n"); } // Run information SealType sealType = (SealType) sess.get(SealType.class, ir.getCodeSealType()); String sealTypeText = sealType.getSealType(); String plateID = ""; if (codeReactionType.equals(ReactionType.SEQUENCING_REACTION_TYPE)) { plateID = runName; } else { plateID = idInstrumentRun.toString(); } String owner = ""; AppUser user = (AppUser) sess.get(AppUser.class, Integer.valueOf(ir.getCreator())); owner = user.getShortName() != null ? user.getShortName() : "Core"; if (codeReactionType.equals(ReactionType.SEQUENCING_REACTION_TYPE)) { response .getOutputStream() .print( runName + "\t" + plateID + "\t\tSequencingAnalysis\t384-Well\t" + owner + "\t3730-1\t" + sealTypeText + "\t1234\t\r\n"); } else if (codeReactionType.equals(ReactionType.MITO_DLOOP_REACTION_TYPE)) { response .getOutputStream() .print( runName + "\t" + plateID + "\t\tSequencingAnalysis\t384-Well\t" + owner + "\t" + owner + "\t" + sealTypeText + "\t1234\t\r\n"); } else { response .getOutputStream() .print( runName + "\t" + plateID + "\t\t384-Well\tRegular\t" + owner + "\t" + owner + "\t" + sealTypeText + "\t1234\t\n"); response.getOutputStream().print("AppServer\tAppInstance\t\n"); response.getOutputStream().print("GeneMapper\tGeneMapper_Generic_Instance\t\n"); } // Well headers if (codeReactionType.equals(ReactionType.FRAGMENT_ANALYSIS_REACTION_TYPE)) { response .getOutputStream() .print( "Well\tSample Name\tComment\tSampleType\tSnp Set\tAnalysis Method\tPanel" + "\tUser-Defined 3\tSize Standard" + "\tUser-Defined 2\tUser-Defined 1" + "\tResults Group 1\tInstrument Protocol 1" + "\tResults Group 2\tInstrument Protocol 2" + "\tResults Group 3\tInstrument Protocol 3" + "\tResults Group 4\tInstrument Protocol 4" + "\tResults Group 5\tInstrument Protocol 5\t\r\n"); } else { response .getOutputStream() .print( "Well\tSample Name\tComment\tResults Group" + "\tInstrument Protocol 1\tAnalysis Protocol 1" + "\tInstrument Protocol 2\tAnalysis Protocol 2" + "\tInstrument Protocol 3\tAnalysis Protocol 3" + "\tInstrument Protocol 4\tAnalysis Protocol 4" + "\tInstrument Protocol 5\tAnalysis Protocol 5\t\r\n"); } Element runNode = getRunWells(sess); if (runNode != null) { Iterator i = runNode.getChildren("PlateWell").iterator(); for (char row = 'A'; row <= 'P'; row++) { for (int col = 1; col <= 24; col++) { if (i.hasNext()) { Element well = (Element) i.next(); String idPlateWellString = well.getAttributeValue("idPlateWell") != null ? well.getAttributeValue("idPlateWell") : "0"; String sampleName = well.getAttributeValue("sampleName") != null ? well.getAttributeValue("sampleName") : ""; if (well.getAttributeValue("isControl") != null && well.getAttributeValue("isControl").equals("Y")) { sampleName = "pGem"; } String idSample = well.getAttributeValue("idSample") != null ? well.getAttributeValue("idSample") : ""; String idPlate = well.getAttributeValue("idPlate") != null ? well.getAttributeValue("idPlate") : ""; String primer = well.getAttributeValue("primer") != null ? well.getAttributeValue("primer") : ""; String assay = well.getAttributeValue("assay") != null ? well.getAttributeValue("assay") : ""; String wellRow = well.getAttributeValue("row") != null ? well.getAttributeValue("row") : ""; int wellCol = well.getAttributeValue("col") != null ? Integer.valueOf(well.getAttributeValue("col")) : 0; if (idPlateWellString != null && !idPlateWellString.equals("0")) { if (well.getAttributeValue("isControl") != null && well.getAttributeValue("isControl").equals("Y")) { idSample = idPlateWellString; } response.getOutputStream().print(row + String.format("%02d", col) + "\t"); String fileName; if (codeReactionType.equals(ReactionType.SEQUENCING_REACTION_TYPE)) { fileName = sampleName; fileName = fileName.replaceAll("\\s", "_"); response.getOutputStream().print(fileName + "\t"); } else if (codeReactionType.equals(ReactionType.MITO_DLOOP_REACTION_TYPE)) { fileName = sampleName + "_" + primer; fileName = fileName.replaceAll("\\s", "_"); response.getOutputStream().print(fileName + "\t"); } else if (codeReactionType.equals( ReactionType.FRAGMENT_ANALYSIS_REACTION_TYPE)) { fileName = sampleName + "_" + assay; fileName = fileName.replaceAll("\\s", "_"); response.getOutputStream().print(fileName + "\t"); } String comments = "<ID:" + idPlateWellString + ">"; if (codeReactionType.equals(ReactionType.SEQUENCING_REACTION_TYPE)) { comments += "<WELL:" + wellRow + String.format("%02d", wellCol) + ">"; } response.getOutputStream().print(comments + "\t"); if (codeReactionType.equals(ReactionType.SEQUENCING_REACTION_TYPE)) { response.getOutputStream().print("HCI\tLongSeq50\tSeq_A\t\r\n"); } else if (codeReactionType.equals(ReactionType.MITO_DLOOP_REACTION_TYPE)) { response.getOutputStream().print("HCI\tLongSeq50\tPCR\t\r\n"); } else if (codeReactionType.equals( ReactionType.FRAGMENT_ANALYSIS_REACTION_TYPE)) { response .getOutputStream() .print("\t\t\t\t\t\t\t\tHCI\tFragAnalysis-RCT_50_POP7\t\n"); } } } } } } out.close(); out.flush(); } else { response.setContentType("text/html"); response.getOutputStream().println("<html><head><title>Error</title></head>"); response.getOutputStream().println("<body><b>"); response .getOutputStream() .println( "DownloadABIRunFileServlet: You must have a SecurityAdvisor in order to run this command." + "<br>"); response.getOutputStream().println("</body>"); response.getOutputStream().println("</html>"); System.out.println( "DownloadABIRunFileServlet: You must have a SecurityAdvisor in order to run this command."); } } catch (Exception e) { LOG.error("Exception in DownloadABIRunFileServlet: ", e); HibernateSession.rollback(); response.setContentType("text/html"); response.getOutputStream().println("<html><head><title>Error</title></head>"); response.getOutputStream().println("<body><b>"); response .getOutputStream() .println("DownloadABIRunFileServlet: An exception occurred " + e.toString() + "<br>"); response.getOutputStream().println("</body>"); response.getOutputStream().println("</html>"); } finally { try { secAdvisor.closeHibernateSession(); } catch (Exception e) { LOG.error("Exception in DownloadABIRunFileServlet: ", e); } } }