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);
}
}
}