public Command execute() throws RollBackCommandException {
try {
Session sess = this.getSecAdvisor().getReadOnlyHibernateSession(this.getUsername());
DictionaryHelper dh = DictionaryHelper.getInstance(sess);
HashMap statusNodeMap = new HashMap();
if (billingItemFilter.getIdBillingPeriod() != null) {
BillingPeriod bp = dh.getBillingPeriod(billingItemFilter.getIdBillingPeriod());
if (bp == null) {
throw new RollBackCommandException(
"Unable to find billing period " + billingItemFilter.getIdBillingPeriod());
}
billingItemFilter.setBillingPeriod(bp);
}
StringBuffer buf = billingItemFilter.getBillingNewRequestQuery();
LOG.info("Query: " + buf.toString());
List newRequests = sess.createQuery(buf.toString()).list();
Element statusNode = new Element("Status");
TreeMap requestToStatusMap = new TreeMap(new RequestNumberBilledComparator());
HashMap requestNodeMap = new HashMap();
HashMap statusToLabNodeMap = new HashMap();
// Query all requests that don't have any billing items.
// Assign these requests a 'Pending' status.
if (newRequests.size() > 0) {
statusNode.setAttribute("label", "Pending");
statusNode.setAttribute("status", BillingStatus.PENDING);
statusNodeMap.put(BillingStatus.PENDING, statusNode);
for (Iterator i = newRequests.iterator(); i.hasNext(); ) {
Object[] row = (Object[]) i.next();
Integer idRequest = (Integer) row[0];
String requestNumber = (String) row[1] == null ? "" : (String) row[1];
String codeRequestCategory = (String) row[2] == null ? "" : (String) row[2];
String idBillingAccount = (Integer) row[3] == null ? "" : ((Integer) row[3]).toString();
String labLastName = (String) row[4] == null ? "" : (String) row[4];
String labFirstName = (String) row[5] == null ? "" : (String) row[5];
AppUser submitter = (AppUser) row[6];
java.util.Date createDate = (java.util.Date) row[7];
Date completedDate = (Date) row[8];
BillingAccount billingAcct = (BillingAccount) row[9];
String labIsExternalPricing = (String) row[10];
String labIsExternalPricingCommercial = (String) row[11];
String labName = Lab.formatLabName(labLastName, labFirstName);
String toolTip = requestNumber + " " + labName;
if (createDate != null) {
toolTip += "\nsubmitted " + this.formatDate(createDate, this.DATE_OUTPUT_DASH_SHORT);
}
if (completedDate != null) {
toolTip +=
", completed " + this.formatDate(completedDate, this.DATE_OUTPUT_DASH_SHORT);
}
RequestCategory requestCategory = dh.getRequestCategoryObject(codeRequestCategory);
Element node = new Element("Request");
node.setAttribute("idRequest", idRequest.toString());
node.setAttribute("idProductOrder", "");
node.setAttribute("requestNumber", requestNumber);
node.setAttribute("label", requestNumber);
node.setAttribute("codeRequestCategory", codeRequestCategory);
node.setAttribute(
"icon",
requestCategory != null && requestCategory.getIcon() != null
? requestCategory.getIcon()
: "");
node.setAttribute(
"type",
requestCategory != null && requestCategory.getType() != null
? requestCategory.getType()
: "");
node.setAttribute("idBillingAccount", idBillingAccount);
node.setAttribute("labName", labName != null ? labName : "");
node.setAttribute("toolTip", toolTip);
node.setAttribute("submitter", submitter != null ? submitter.getDisplayName() : "");
node.setAttribute("codeBillingStatus", BillingStatus.NEW);
node.setAttribute(
"createDate",
createDate != null ? this.formatDate(createDate, this.DATE_OUTPUT_DASH) : "");
node.setAttribute(
"completedDate",
completedDate != null ? this.formatDate(completedDate, this.DATE_OUTPUT_DASH) : "");
node.setAttribute(
"isExternalPricing", labIsExternalPricing != null ? labIsExternalPricing : "N");
node.setAttribute(
"isExternalPricingCommercial",
labIsExternalPricingCommercial != null ? labIsExternalPricingCommercial : "N");
node.setAttribute("hasBillingItems", "N");
String labBillingName = labName;
if (billingAcct != null) {
labBillingName += " (" + billingAcct.getAccountNameAndNumber() + ")";
}
String requestNumberBilled = requestNumber + DELIM + labBillingName;
// Hash the status node.
List statusList = (List) requestToStatusMap.get(requestNumberBilled);
if (statusList == null) {
statusList = new ArrayList<String>();
requestToStatusMap.put(requestNumberBilled, statusList);
}
statusList.add(BillingStatus.PENDING);
// There can be multiple requests nodes for a given request number when
// the request's billing items are split among multiple billing
// accounts. Keep a hash map of these different request nodes.
TreeMap requestNodes = (TreeMap) requestNodeMap.get(requestNumberBilled);
if (requestNodes == null) {
requestNodes = new TreeMap(new RequestNumberBilledComparator());
requestNodeMap.put(requestNumberBilled, requestNodes);
}
requestNodes.put(requestNumberBilled, node);
}
}
buf = billingItemFilter.getBillingRequestQuery();
LOG.info("Query: " + buf.toString());
List billingItemRequests = sess.createQuery(buf.toString()).list();
String prevCodeBillingStatus = "NEW";
//
// Query all requests with billing items. Determine status by looking
// at all of billing items for request.
// Hash nodes for lab/billing account, status.
//
for (Iterator i = billingItemRequests.iterator(); i.hasNext(); ) {
Object[] row = (Object[]) i.next();
String codeBillingStatus = (String) row[0] == null ? "" : (String) row[0];
Integer idRequest = (Integer) row[1];
String requestNumber = (String) row[2] == null ? "" : (String) row[2];
String codeRequestCategory = (String) row[3] == null ? "" : (String) row[3];
Integer idLab = (Integer) row[4];
String labLastName = (String) row[5] == null ? "" : (String) row[5];
String labFirstName = (String) row[6] == null ? "" : (String) row[6];
AppUser submitter = (AppUser) row[7];
java.util.Date createDate = (java.util.Date) row[8];
Date completedDate = (Date) row[9];
BillingAccount billingAcct = (BillingAccount) row[10];
String labIsExternalPricing = (String) row[11];
String labIsExternalPricingCommercial = (String) row[12];
Integer idInvoice = (Integer) row[13];
String contactEmail = (String) row[14];
String billingContactEmail = (String) row[15];
String labName = Lab.formatLabName(labLastName, labFirstName);
String billingEmail = Lab.formatBillingNotificationEmail(contactEmail, billingContactEmail);
String toolTip = requestNumber + " " + labName;
String labBillingName = labName + " (" + billingAcct.getAccountNameAndNumber() + ")";
String requestNumberBilled = requestNumber + DELIM + labBillingName;
if (createDate != null) {
toolTip += "\nsubmitted " + this.formatDate(createDate, this.DATE_OUTPUT_DASH_SHORT);
}
if (completedDate != null) {
toolTip += ", completed " + this.formatDate(completedDate, this.DATE_OUTPUT_DASH_SHORT);
}
List statusList = (List) requestToStatusMap.get(requestNumberBilled);
if (statusList == null) {
statusList = new ArrayList<String>();
requestToStatusMap.put(requestNumberBilled, statusList);
}
statusList.add(codeBillingStatus);
Map labNodeMap = (Map) statusToLabNodeMap.get(codeBillingStatus);
if (labNodeMap == null) {
labNodeMap = new TreeMap();
statusToLabNodeMap.put(codeBillingStatus, labNodeMap);
}
Element labNode = (Element) labNodeMap.get(labBillingName);
if (labNode == null) {
labNode = new Element("Lab");
labNode.setAttribute("label", labBillingName);
labNode.setAttribute("dataTip", labBillingName);
labNode.setAttribute("idLab", idLab != null ? idLab.toString() : "");
labNode.setAttribute("name", labName);
labNode.setAttribute("idBillingAccount", billingAcct.getIdBillingAccount().toString());
labNode.setAttribute("billingAccountName", billingAcct.getAccountNameAndNumber());
labNode.setAttribute("contactEmail", contactEmail != null ? contactEmail : "");
labNode.setAttribute(
"billingNotificationEmail", billingEmail != null ? billingEmail : "");
if (idInvoice != null) {
labNode.setAttribute("idInvoice", idInvoice.toString());
}
labNodeMap.put(labBillingName, labNode);
}
if (!prevCodeBillingStatus.equals(codeBillingStatus)) {
statusNode = new Element("Status");
statusNode.setAttribute("label", dh.getBillingStatus(codeBillingStatus));
statusNode.setAttribute("status", codeBillingStatus);
statusNodeMap.put(codeBillingStatus, statusNode);
}
RequestCategory requestCategory = dh.getRequestCategoryObject(codeRequestCategory);
Element node = new Element("Request");
node.setAttribute("idRequest", idRequest.toString());
node.setAttribute("idProductOrder", "");
node.setAttribute("label", requestNumber);
node.setAttribute("requestNumber", requestNumber);
node.setAttribute("toolTip", toolTip);
node.setAttribute("codeRequestCategory", codeRequestCategory);
node.setAttribute(
"icon",
requestCategory != null && requestCategory.getIcon() != null
? requestCategory.getIcon()
: "");
node.setAttribute(
"type",
requestCategory != null && requestCategory.getType() != null
? requestCategory.getType()
: "");
node.setAttribute("submitter", submitter != null ? submitter.getDisplayName() : "");
node.setAttribute("labBillingName", labBillingName);
node.setAttribute("idLab", idLab != null ? idLab.toString() : "");
node.setAttribute("labName", labName != null ? labName : "");
node.setAttribute("idBillingAccount", billingAcct.getIdBillingAccount().toString());
node.setAttribute("billingAccountName", billingAcct.getAccountNameAndNumber());
node.setAttribute(
"isExternalPricing", labIsExternalPricing != null ? labIsExternalPricing : "N");
node.setAttribute(
"isExternalPricingCommercial",
labIsExternalPricingCommercial != null ? labIsExternalPricingCommercial : "N");
node.setAttribute("hasBillingItems", "Y");
if (idInvoice != null) {
node.setAttribute("idInvoice", idInvoice.toString());
}
// There can be multiple requests nodes for a given request number when
// the request's billing items are split among multiple billing
// accounts. Keep a hash map of these different request nodes.
TreeMap requestNodes = (TreeMap) requestNodeMap.get(requestNumberBilled);
if (requestNodes == null) {
requestNodes = new TreeMap(new RequestNumberBilledComparator());
requestNodeMap.put(requestNumberBilled, requestNodes);
}
requestNodes.put(requestNumberBilled, node);
prevCodeBillingStatus = codeBillingStatus;
}
buf = billingItemFilter.getBillingDiskUsageQuery();
LOG.info("Query: " + buf.toString());
List billingItemDiskUsage = sess.createQuery(buf.toString()).list();
prevCodeBillingStatus = "NEW";
//
// Query all disk usage rows with billing items. Determine status by looking
// at all of billing items for disk usage (should only be one but...)
// Hash nodes for lab/billing account, status.
//
for (Iterator i = billingItemDiskUsage.iterator(); i.hasNext(); ) {
Object[] row = (Object[]) i.next();
String codeBillingStatus = (String) row[0] == null ? "" : (String) row[0];
Integer idDiskUsage = (Integer) row[1];
Integer idLab = (Integer) row[2];
String labLastName = (String) row[3] == null ? "" : (String) row[3];
String labFirstName = (String) row[4] == null ? "" : (String) row[4];
java.util.Date asOfDate = (java.util.Date) row[5];
BillingAccount billingAcct = (BillingAccount) row[6];
String labIsExternalPricing = (String) row[7];
String labIsExternalPricingCommercial = (String) row[8];
Integer idInvoice = (Integer) row[9];
String contactEmail = (String) row[10];
String labName = Lab.formatLabName(labLastName, labFirstName);
String toolTip = "Disk Usage Charge for " + labName;
String labBillingName = labName + " (" + billingAcct.getAccountNameAndNumber() + ")";
String requestNumberBilled =
DISK_USAGE_PREFIX + idDiskUsage.toString() + DELIM + labBillingName;
if (asOfDate != null) {
toolTip += "\ncomputed as of " + this.formatDate(asOfDate, this.DATE_OUTPUT_DASH_SHORT);
}
List statusList = (List) requestToStatusMap.get(requestNumberBilled);
if (statusList == null) {
statusList = new ArrayList<String>();
requestToStatusMap.put(requestNumberBilled, statusList);
}
statusList.add(codeBillingStatus);
Map labNodeMap = (Map) statusToLabNodeMap.get(codeBillingStatus);
if (labNodeMap == null) {
labNodeMap = new TreeMap();
statusToLabNodeMap.put(codeBillingStatus, labNodeMap);
}
Element labNode = (Element) labNodeMap.get(labBillingName);
if (labNode == null) {
labNode = new Element("Lab");
labNode.setAttribute("label", labBillingName);
labNode.setAttribute("dataTip", labBillingName);
labNode.setAttribute("idLab", idLab != null ? idLab.toString() : "");
labNode.setAttribute("name", labName);
labNode.setAttribute("idBillingAccount", billingAcct.getIdBillingAccount().toString());
labNode.setAttribute("billingAccountName", billingAcct.getAccountNameAndNumber());
labNode.setAttribute("contactEmail", contactEmail != null ? contactEmail : "");
if (idInvoice != null) {
labNode.setAttribute("idInvoice", idInvoice.toString());
}
labNodeMap.put(labBillingName, labNode);
}
if (!prevCodeBillingStatus.equals(codeBillingStatus)) {
if (!statusNodeMap.containsKey(codeBillingStatus)) {
statusNode = new Element("Status");
statusNode.setAttribute("label", dh.getBillingStatus(codeBillingStatus));
statusNode.setAttribute("status", codeBillingStatus);
statusNodeMap.put(codeBillingStatus, statusNode);
} else {
statusNode = (Element) statusNodeMap.get(codeBillingStatus);
}
}
Element node = new Element("Request");
node.setAttribute("idRequest", idDiskUsage.toString());
node.setAttribute("idProductOrder", "");
node.setAttribute("label", "Disk Usage");
node.setAttribute("requestNumber", "Disk Usage");
node.setAttribute("toolTip", toolTip);
node.setAttribute("codeRequestCategory", DiskUsageByMonth.DISK_USAGE_REQUEST_CATEGORY);
node.setAttribute("icon", DiskUsageByMonth.DISK_USAGE_ICON);
node.setAttribute("type", "Disk Usage");
node.setAttribute("submitter", "");
node.setAttribute("labBillingName", labBillingName);
node.setAttribute("idLab", idLab != null ? idLab.toString() : "");
node.setAttribute("labName", labName != null ? labName : "");
node.setAttribute("idBillingAccount", billingAcct.getIdBillingAccount().toString());
node.setAttribute("billingAccountName", billingAcct.getAccountNameAndNumber());
node.setAttribute(
"isExternalPricing", labIsExternalPricing != null ? labIsExternalPricing : "N");
node.setAttribute(
"isExternalPricingCommercial",
labIsExternalPricingCommercial != null ? labIsExternalPricingCommercial : "N");
node.setAttribute("hasBillingItems", "Y");
if (idInvoice != null) {
node.setAttribute("idInvoice", idInvoice.toString());
}
// There can be multiple requests nodes for a given request number when
// the request's billing items are split among multiple billing
// accounts. This should never happen for disk usage, but keeping the code anyway.
TreeMap requestNodes = (TreeMap) requestNodeMap.get(requestNumberBilled);
if (requestNodes == null) {
requestNodes = new TreeMap(new RequestNumberBilledComparator());
requestNodeMap.put(requestNumberBilled, requestNodes);
}
requestNodes.put(requestNumberBilled, node);
prevCodeBillingStatus = codeBillingStatus;
}
buf = billingItemFilter.getBillingProductOrderQuery();
LOG.info("Query: " + buf.toString());
List billingItemProductOrder = sess.createQuery(buf.toString()).list();
prevCodeBillingStatus = "NEW";
List labNames = new ArrayList();
//
// Query all product order rows with billing items. Determine status by looking
// at all of billing items for product order (should only be one but...)
// Hash nodes for lab/billing account, status.
//
for (Iterator i = billingItemProductOrder.iterator(); i.hasNext(); ) {
Object[] row = (Object[]) i.next();
String codeBillingStatus = (String) row[0] == null ? "" : (String) row[0];
String productOrderNumber = (String) row[1] == null ? "" : (String) row[1];
Integer idProductOrder = (Integer) row[2];
Integer idLab = (Integer) row[3];
String labLastName = (String) row[4] == null ? "" : (String) row[4];
String labFirstName = (String) row[5] == null ? "" : (String) row[5];
java.util.Date submitDate = (java.util.Date) row[6];
BillingAccount billingAcct = (BillingAccount) row[7];
String labIsExternalPricing = (String) row[8];
String labIsExternalPricingCommercial = (String) row[9];
Integer idInvoice = (Integer) row[10];
String contactEmail = (String) row[11];
Integer idCoreFacility = (Integer) row[12];
String labName = Lab.formatLabName(labLastName, labFirstName);
String toolTip = "Product Order Charge for " + labName;
String labBillingName = labName + " (" + billingAcct.getAccountNameAndNumber() + ")";
String requestNumberBilled =
PRODUCT_ORDER_PREFIX + idProductOrder.toString() + DELIM + labBillingName;
if (submitDate != null) {
toolTip += "\nsubmitted on " + this.formatDate(submitDate, this.DATE_OUTPUT_DASH_SHORT);
}
List statusList = (List) requestToStatusMap.get(requestNumberBilled);
if (statusList == null) {
statusList = new ArrayList<String>();
requestToStatusMap.put(requestNumberBilled, statusList);
}
statusList.add(codeBillingStatus);
Map labNodeMap = (Map) statusToLabNodeMap.get(codeBillingStatus);
if (labNodeMap == null) {
labNodeMap = new TreeMap();
statusToLabNodeMap.put(codeBillingStatus, labNodeMap);
}
Element labNode = (Element) labNodeMap.get(labBillingName);
if (labNode == null) {
labNode = new Element("Lab");
labNode.setAttribute("label", labBillingName);
labNode.setAttribute("dataTip", labBillingName);
labNode.setAttribute("idLab", idLab != null ? idLab.toString() : "");
labNode.setAttribute("name", labName);
labNode.setAttribute("idBillingAccount", billingAcct.getIdBillingAccount().toString());
labNode.setAttribute("billingAccountName", billingAcct.getAccountNameAndNumber());
labNode.setAttribute("contactEmail", contactEmail != null ? contactEmail : "");
if (idInvoice != null) {
labNode.setAttribute("idInvoice", idInvoice.toString());
}
labNodeMap.put(labBillingName, labNode);
}
if (!prevCodeBillingStatus.equals(codeBillingStatus)) {
if (!statusNodeMap.containsKey(codeBillingStatus)) {
statusNode = new Element("Status");
statusNode.setAttribute("label", dh.getBillingStatus(codeBillingStatus));
statusNode.setAttribute("status", codeBillingStatus);
statusNodeMap.put(codeBillingStatus, statusNode);
} else {
statusNode = (Element) statusNodeMap.get(codeBillingStatus);
}
}
Element node = new Element("Request");
node.setAttribute("idRequest", idProductOrder.toString());
node.setAttribute("idProductOrder", idProductOrder.toString());
node.setAttribute("idCoreFacility", idCoreFacility.toString());
node.setAttribute(
"label",
"Product Order "
+ (productOrderNumber.equals("") ? idProductOrder.toString() : productOrderNumber));
node.setAttribute(
"requestNumber",
productOrderNumber.equals("") ? idProductOrder.toString() : productOrderNumber);
node.setAttribute("toolTip", toolTip);
node.setAttribute("codeRequestCategory", ProductOrder.PRODUCT_ORDER_REQUEST_CATEGORY);
node.setAttribute("icon", ProductOrder.PRODUCT_ORDER_ICON);
node.setAttribute("type", "Product Order");
node.setAttribute("submitter", "");
node.setAttribute("labBillingName", labBillingName);
node.setAttribute("idLab", idLab != null ? idLab.toString() : "");
node.setAttribute("labName", labName != null ? labName : "");
node.setAttribute("idBillingAccount", billingAcct.getIdBillingAccount().toString());
node.setAttribute("billingAccountName", billingAcct.getAccountNameAndNumber());
node.setAttribute(
"isExternalPricing", labIsExternalPricing != null ? labIsExternalPricing : "N");
node.setAttribute(
"isExternalPricingCommercial",
labIsExternalPricingCommercial != null ? labIsExternalPricingCommercial : "N");
node.setAttribute("hasBillingItems", "Y");
if (idInvoice != null) {
node.setAttribute("idInvoice", idInvoice.toString());
}
// There can be multiple requests nodes for a given request number when
// the request's billing items are split among multiple billing
// accounts. This should never happen for disk usage, but keeping the code anyway.
TreeMap requestNodes = (TreeMap) requestNodeMap.get(requestNumberBilled);
if (requestNodes == null) {
requestNodes = new TreeMap(new RequestNumberBilledComparator());
requestNodeMap.put(requestNumberBilled, requestNodes);
}
requestNodes.put(requestNumberBilled, node);
labNames.add(labBillingName);
prevCodeBillingStatus = codeBillingStatus;
}
//
// Determine request status.
// - If any billing items are Pending, status is Pending.
// - If any billing items are Completed, status is Completed.
// - If all billing items are approved, status is Approved.
//
// Organize requests under lab/billing account node if request is Completed or Approved; and
// then place lab/billing account nodes under appropriate status node).
// Organize requests directly under status node if request is Pending.
//
for (Iterator i = requestToStatusMap.keySet().iterator(); i.hasNext(); ) {
String requestNumberBilled = (String) i.next();
List statusList = (List) requestToStatusMap.get(requestNumberBilled);
Map requestNodes = (Map) requestNodeMap.get(requestNumberBilled);
if (requestNodes == null) {
System.out.println("Cannot find request nodes for " + requestNumberBilled);
continue;
}
// For this request, figure out which of the billing item
// status takes precedence.
String codeBillingStatus = null;
if (statusList.size() == 1) {
codeBillingStatus = (String) statusList.iterator().next();
} else {
// Pending takes precedence over completed, approved
// Then completed takes precedence over approved
for (Iterator i1 = statusList.iterator(); i1.hasNext(); ) {
String code = (String) i1.next();
if (code.equals(BillingStatus.PENDING)) {
codeBillingStatus = code;
break;
}
}
if (codeBillingStatus == null) {
for (Iterator i1 = statusList.iterator(); i1.hasNext(); ) {
String code = (String) i1.next();
if (code.equals(BillingStatus.COMPLETED)) {
codeBillingStatus = code;
break;
}
}
}
if (codeBillingStatus == null) {
for (Iterator i1 = statusList.iterator(); i1.hasNext(); ) {
String code = (String) i1.next();
if (code.equals(BillingStatus.APPROVED)) {
codeBillingStatus = code;
break;
}
}
}
if (codeBillingStatus == null) {
for (Iterator i1 = statusList.iterator(); i1.hasNext(); ) {
String code = (String) i1.next();
if (code.equals(BillingStatus.APPROVED_PO)) {
codeBillingStatus = code;
break;
}
}
}
if (codeBillingStatus == null) {
for (Iterator i1 = statusList.iterator(); i1.hasNext(); ) {
String code = (String) i1.next();
if (code.equals(BillingStatus.APPROVED_CC)) {
codeBillingStatus = code;
break;
}
}
}
}
// Grab the appropriate status node
statusNode = (Element) statusNodeMap.get(codeBillingStatus);
// If the status is PENDING, only stick one request node
// under pending (don't consider distinct billing accounts for
// billing items under a request.)
if (codeBillingStatus.equals(BillingStatus.PENDING)) {
String key = (String) requestNodes.keySet().iterator().next();
Element requestNode = (Element) requestNodes.get(key);
statusNode.addContent(requestNode);
} else {
// If the status is COMPLETED or APPROVED,
// For each request/billing account combination, attach
// the request node to the appropriate parent lab/billing
// account node
for (Iterator i0 = requestNodes.keySet().iterator(); i0.hasNext(); ) {
String key = (String) i0.next();
Element requestNode = (Element) requestNodes.get(key);
Map labNodeMap = (Map) statusToLabNodeMap.get(codeBillingStatus);
Element labNode =
(Element) labNodeMap.get(requestNode.getAttributeValue("labBillingName"));
if (labNode == null) {
labNode = new Element("Lab");
labNode.setAttribute("label", requestNode.getAttributeValue("labBillingName"));
labNode.setAttribute("dataTip", requestNode.getAttributeValue("labBillingName"));
labNode.setAttribute("idLab", requestNode.getAttributeValue("idLab"));
labNode.setAttribute("name", requestNode.getAttributeValue("labBillingName"));
labNode.setAttribute(
"idBillingAccount", requestNode.getAttributeValue("idBillingAccount"));
labNode.setAttribute(
"billingAccountName", requestNode.getAttributeValue("billingAccountName"));
labNodeMap.put(requestNode.getAttributeValue("labBillingName"), labNode);
labNode.addContent(requestNode);
} else {
labNode.addContent(requestNode);
}
}
}
}
// Now create XML document organizing each request
// under <STATUS> node. Show <STATUS> in order
// of New, Pending, Completed, Approved.
Document doc = new Document(new Element("BillingRequestList"));
Element status = (Element) statusNodeMap.get(BillingStatus.NEW);
if (status != null) {
doc.getRootElement().addContent(status);
}
status = (Element) statusNodeMap.get(BillingStatus.PENDING);
if (status != null) {
doc.getRootElement().addContent(status);
}
status = (Element) statusNodeMap.get(BillingStatus.COMPLETED);
if (status != null) {
doc.getRootElement().addContent(status);
// Add non-empty labNodes onto status
Map labNodeMap = (Map) statusToLabNodeMap.get(BillingStatus.COMPLETED);
for (Iterator i1 = labNodeMap.keySet().iterator(); i1.hasNext(); ) {
String key = (String) i1.next();
Element labNode = (Element) labNodeMap.get(key);
if (labNode.hasChildren()) {
status.addContent(labNode);
}
}
}
status = (Element) statusNodeMap.get(BillingStatus.APPROVED_CC);
if (status != null) {
doc.getRootElement().addContent(status);
// Add non-empty labNodes onto status
Map labNodeMap = (Map) statusToLabNodeMap.get(BillingStatus.APPROVED_CC);
for (Iterator i1 = labNodeMap.keySet().iterator(); i1.hasNext(); ) {
String key = (String) i1.next();
Element labNode = (Element) labNodeMap.get(key);
if (labNode.hasChildren()) {
status.addContent(labNode);
}
}
}
status = (Element) statusNodeMap.get(BillingStatus.APPROVED_PO);
if (status != null) {
doc.getRootElement().addContent(status);
// Add non-empty labNodes onto status
Map labNodeMap = (Map) statusToLabNodeMap.get(BillingStatus.APPROVED_PO);
for (Iterator i1 = labNodeMap.keySet().iterator(); i1.hasNext(); ) {
String key = (String) i1.next();
Element labNode = (Element) labNodeMap.get(key);
if (labNode.hasChildren()) {
status.addContent(labNode);
}
}
}
status = (Element) statusNodeMap.get(BillingStatus.APPROVED);
if (status != null) {
doc.getRootElement().addContent(status);
// Add non-empty labNodes onto status
Map labNodeMap = (Map) statusToLabNodeMap.get(BillingStatus.APPROVED);
for (Iterator i1 = labNodeMap.keySet().iterator(); i1.hasNext(); ) {
String key = (String) i1.next();
Element labNode = (Element) labNodeMap.get(key);
if (labNode.hasChildren()) {
status.addContent(labNode);
}
}
}
XMLOutputter out = new org.jdom.output.XMLOutputter();
this.xmlResult = out.outputString(doc);
setResponsePage(this.SUCCESS_JSP);
} catch (Exception e) {
LOG.error("An exception has occurred in GetBillingRequestList ", e);
throw new RollBackCommandException(e.getMessage());
} finally {
try {
// closeReadOnlyHibernateSession;
} catch (Exception e) {
LOG.error("An exception has occurred in GetBillingRequestList ", e);
}
}
return this;
}
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);
}
}
}
