/**
* Returns the full details of the tissue samples with the specified IDs. One or more columns must
* be specified before calling this method. The only filters are the sample IDs that are passed to
* this method.
*
* @param sampleIds the array of sample IDs
* @return A <code>List</code> of {@link com.ardais.bigr.javabeans.SampleData} beans.
*/
public List getDetails(String[] sampleIds) {
List sampleDataBeans = new ArrayList();
Map sampleMap = new HashMap();
int numIds = sampleIds.length;
for (int i = 0; i < numIds; i++) {
String id = sampleIds[i];
SampleData sample = new SampleData();
sample.setSampleId(id);
sampleMap.put(id, sample);
sampleDataBeans.add(sample);
}
getDetails(sampleMap);
return sampleDataBeans;
}
/** Insert the method's description here. Creation date: (2/2/2001 2:39:22 PM) */
public void invoke() throws Exception {
SecurityInfo securityInfo = WebUtils.getSecurityInfo(request);
// Check if box layout is valid for this account.
String boxLayoutId = request.getParameter("boxLayoutId");
boxLayoutId = BoxLayoutUtils.checkBoxLayoutId(boxLayoutId, false, true, true);
if (!ApiFunctions.isEmpty(boxLayoutId)) {
String accountId = securityInfo.getAccount();
if (!BoxLayoutUtils.isValidBoxLayoutForAccount(boxLayoutId, accountId)) {
// The box layout id is not part of the account box layout group.
retry("The box layout selected does not belong to this account.");
}
}
BoxLayoutDto boxLayoutDto = BoxLayoutUtils.getBoxLayoutDto(boxLayoutId);
request.setAttribute("boxLayoutDto", boxLayoutDto);
// Scan through all of the box cells to find the sample ids and/or aliases.
// Here we're just accumulating non-null entries, we do validation later.
//
HashMap sampleNumberToSample = new HashMap();
for (int i = 0; i < boxLayoutDto.getBoxCapacity(); i++) {
String sampleNumber = "smpl" + (i + 1);
String sampleIdOrAlias = ApiFunctions.safeString(request.getParameter(sampleNumber)).trim();
if (!ApiFunctions.isEmpty(sampleIdOrAlias)) {
sampleNumberToSample.put(sampleNumber, sampleIdOrAlias);
}
}
// Get relevant information about the samples, and populate the request with that information.
// If there was a problem getting the information return an error (but populate any retrieved
// sample information first so it is retained for existing samples)
String error = getSampleInfo(sampleNumberToSample, securityInfo);
for (int i = 0; i < boxLayoutDto.getBoxCapacity(); i++) {
String sampleNumber = "smpl" + (i + 1);
String sampleIdOrAlias = ApiFunctions.safeString(request.getParameter(sampleNumber)).trim();
if (!ApiFunctions.isEmpty(sampleIdOrAlias)) {
SampleData sample = (SampleData) sampleNumberToSample.get(sampleNumber);
request.setAttribute("smplType" + (i + 1), sample.getSampleType());
request.setAttribute("smplAlias" + (i + 1), sample.getSampleAlias());
}
}
if (!ApiFunctions.isEmpty(error)) {
retry(error);
return;
}
// iterate over the samples, gathering data we'll need for additional checking. Note that
// at this point, regardless of whether the sample was scanned via its system id or alias,
// we have retrieved the sample id, sample alias, and sample type for every sample.
List systemSampleIds = new ArrayList();
Iterator i = sampleNumberToSample.keySet().iterator();
while (i.hasNext()) {
String sampleNumber = (String) i.next();
SampleData sample = (SampleData) sampleNumberToSample.get(sampleNumber);
if (sample != null) {
String sampleId = sample.getSampleId();
systemSampleIds.add(sampleId);
}
}
// SWP-1100 - if nothing has been scanned in, return an error
if (sampleNumberToSample.size() == 0) {
retry("Please enter sample(s) before continuing.");
return;
}
// Now perform some additional checks. Pass true for the check to make sure that samples
// exist, because for a check-out operation we always require that all of the samples
// actually exist. Note however that since we've already performed that check above this check
// should always succeed.
if (!ApiFunctions.isEmpty(systemSampleIds)) {
// MR7356 Don't allow samples on open requests to be scanned into the new box
boolean enforceRequestedSampleRestrictions = true;
SampleOperationHome sampleOpHome =
(SampleOperationHome) EjbHomes.getHome(SampleOperationHome.class);
SampleOperation sampleOp = sampleOpHome.create();
String validSampleSetError =
sampleOp.validSamplesForBoxScan(
systemSampleIds,
true,
enforceRequestedSampleRestrictions,
false,
securityInfo,
boxLayoutDto);
if (validSampleSetError != null) {
retry(validSampleSetError);
return;
}
}
Vector staffNames = new Vector();
String account = securityInfo.getAccount();
ListGeneratorHome home = (ListGeneratorHome) EjbHomes.getHome(ListGeneratorHome.class);
ListGenerator list = home.create();
staffNames = list.lookupArdaisStaffByAccountId(account);
request.setAttribute("staff", staffNames);
servletCtx
.getRequestDispatcher("/hiddenJsps/iltds/storage/checkOutBox/checkOutBoxConfirm.jsp")
.forward(request, response);
}
private String getSampleInfo(HashMap sampleNumberToSample, SecurityInfo securityInfo) {
Set problems = new HashSet();
List encounteredAliases = new ArrayList();
Iterator i = sampleNumberToSample.keySet().iterator();
while (i.hasNext()) {
String sampleNumber = (String) i.next();
String sampleIdOrAlias = (String) sampleNumberToSample.get(sampleNumber);
String sampleTypeCui = null;
String sampleAlias = null;
// if the value begins with the prefix for any of our sample ids (FR, PA, SX) then
// assume it is a sample id. Return an error if the sample doesn't exist.
if (IltdsUtils.isSystemSampleId(sampleIdOrAlias)) {
try {
SampleAccessBean sample = new SampleAccessBean(new SampleKey(sampleIdOrAlias));
sampleTypeCui = sample.getSampleTypeCid();
sampleAlias = sample.getCustomerId();
} catch (ObjectNotFoundException e) {
StringBuffer error = new StringBuffer(100);
error.append("Sample ");
error.append(sampleIdOrAlias);
error.append(" does not exist in the database.");
problems.add(error.toString());
} catch (Exception e) {
ApiFunctions.throwAsRuntimeException(e);
}
}
// if the value does not begin with the prefix for any of our sample ids (FR, PA, SX) then
// assume it is a sample alias and handle the alias as follows:
// - if the alias corresponds to multiple existing sample ids, return an error.
// - if the alias corresponds to a single existing sample id, see if the account to which that
// sample belongs requires unique aliases.
// - if not, return an error since we cannot be positive the sample we found was the one
// intended.
// - if so
// - if the specified alias has already been encountered return an error since the
// same sample cannot be scanned into multiple locations in a box.
// - if the alias has not yet been encountered then get the information for that
// sample.
// - if the alias corresponds to no existing sample return an error.
else {
// pass false to the findSampleIdsFromCustomerId call, to take into account any samples that
// have been created via a box scan but have not yet been annotated.
List existingSamples = IltdsUtils.findSamplesFromCustomerId(sampleIdOrAlias, false);
// if multiple samples with the specified alias were found, return an error.
if (existingSamples.size() > 1) {
StringBuffer error = new StringBuffer(100);
error.append("The alias \"");
error.append(Escaper.htmlEscapeAndPreserveWhitespace(sampleIdOrAlias));
error.append("\" corresponds to multiple existing samples. Please scan the specific");
error.append(" sample id you wish to use.");
problems.add(error.toString());
}
// if a single sample was found, do some further checking
else if (existingSamples.size() == 1) {
String accountId = ((SampleData) existingSamples.get(0)).getArdaisAcctKey();
AccountDto accountDto = IltdsUtils.getAccountById(accountId, false, false);
boolean aliasMustBeUnique =
FormLogic.DB_YES.equalsIgnoreCase(accountDto.getRequireUniqueSampleAliases());
// if the account to which the sample belongs does not require unique sample aliases,
// return an error since we cannot be sure the sample we found was the one intended.
if (!aliasMustBeUnique) {
StringBuffer error = new StringBuffer(100);
error.append("The alias \"");
error.append(Escaper.htmlEscapeAndPreserveWhitespace(sampleIdOrAlias));
error.append("\" does not uniquely identify a sample.");
error.append(" Please scan the specific sample id you wish to use.");
problems.add(error.toString());
}
// if we've already encountered this alias, return an error (the same sample cannot
// be scanned into multiple locations in a box)
else if (encounteredAliases.contains(sampleIdOrAlias.toUpperCase())) {
StringBuffer error = new StringBuffer(100);
error.append("The alias \"");
error.append(Escaper.htmlEscapeAndPreserveWhitespace(sampleIdOrAlias));
error.append("\" appears more than once.");
problems.add(error.toString());
// still fill in the sample information so the resulting screen looks correct (otherwise
// the first instance of this alias has information but the second does not)
SampleData sample = (SampleData) existingSamples.get(0);
sampleIdOrAlias = sample.getSampleId();
sampleTypeCui = sample.getSampleTypeCui();
sampleAlias = sample.getSampleAlias();
}
// otherwise store the encountered alias (in uppercase, so we can compare subsequent
// aliases to this one without case accounting for any differences) and get the
// information
// for the sample
else {
encounteredAliases.add(sampleIdOrAlias.toUpperCase());
SampleData sample = (SampleData) existingSamples.get(0);
sampleIdOrAlias = sample.getSampleId();
sampleTypeCui = sample.getSampleTypeCui();
sampleAlias = sample.getSampleAlias();
}
}
// if no matching sample was found, return an error
else {
StringBuffer error = new StringBuffer(100);
error.append("Sample \"");
error.append(Escaper.htmlEscapeAndPreserveWhitespace(sampleIdOrAlias));
error.append("\" does not exist in the database.");
problems.add(error.toString());
}
}
// Create a sample data to hold the information
SampleData sample = new SampleData();
sample.setSampleId(sampleIdOrAlias);
sample.setSampleAlias(sampleAlias);
sample.setSampleTypeCui(sampleTypeCui);
if (!ApiFunctions.isEmpty(sampleTypeCui)) {
sample.setSampleType(GbossFactory.getInstance().getDescription(sampleTypeCui));
}
// replace the map entry with the sample data object
sampleNumberToSample.put(sampleNumber, sample);
}
String returnValue = null;
if (!problems.isEmpty()) {
StringBuffer buff = new StringBuffer("The following problems were found: ");
Iterator problemIterator = problems.iterator();
while (problemIterator.hasNext()) {
buff.append((String) problemIterator.next());
buff.append(" ");
}
returnValue = buff.toString();
}
return returnValue;
}
