/**
* 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;
}
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;
}