public Account getAccount(String id) {
id = ApiFunctions.safeTrim(id);
if (ApiFunctions.isEmpty(id)) {
throw new ApiException("A non-empty account id must be specified.");
} else {
return (Account) _accountMap.get(id.toLowerCase());
}
}
/**
* Populates this <code>LocationData</code> from the data in the current row of the result set.
*
* @param columns a <code>Map</code> containing a key for each column in the <code>ResultSet
* </code>. Each key must be one of the column alias constants in {@link
* com.ardais.bigr.util.DbAliases} or {@link com.ardais.bigr.util.DbConstants} or the
* corresponding value is ignored.
* @param rs the <code>ResultSet</code>
*/
public void populate(Map columns, ResultSet rs) {
try {
if (columns.containsKey(DbConstants.LOCATION_ADDRESS_ID)) {
setAddressId(rs.getString(DbConstants.LOCATION_ADDRESS_ID));
}
if (columns.containsKey(DbConstants.LOCATION_NAME)) {
setName(rs.getString(DbConstants.LOCATION_NAME));
}
if (columns.containsKey(DbConstants.LOCATION_ADDRESS_1)) {
setAddress1(rs.getString(DbConstants.LOCATION_ADDRESS_1));
}
if (columns.containsKey(DbConstants.LOCATION_ADDRESS_2)) {
setAddress2(rs.getString(DbConstants.LOCATION_ADDRESS_2));
}
if (columns.containsKey(DbConstants.LOCATION_CITY)) {
setCity(rs.getString(DbConstants.LOCATION_CITY));
}
if (columns.containsKey(DbConstants.LOCATION_STATE)) {
setState(rs.getString(DbConstants.LOCATION_STATE));
}
if (columns.containsKey(DbConstants.LOCATION_ZIP)) {
setZipCode(rs.getString(DbConstants.LOCATION_ZIP));
}
if (columns.containsKey(DbConstants.LOCATION_COUNTRY)) {
setCountry(rs.getString(DbConstants.LOCATION_COUNTRY));
}
if (columns.containsKey(DbConstants.LOCATION_PHONE)) {
setPhoneNumber(rs.getString(DbConstants.LOCATION_PHONE));
}
if (columns.containsKey(DbAliases.LOCATION_ADDRESS_ID)) {
setAddressId(rs.getString(DbAliases.LOCATION_ADDRESS_ID));
}
if (columns.containsKey(DbAliases.LOCATION_NAME)) {
setName(rs.getString(DbAliases.LOCATION_NAME));
}
if (columns.containsKey(DbAliases.LOCATION_ADDRESS_1)) {
setAddress1(rs.getString(DbAliases.LOCATION_ADDRESS_1));
}
if (columns.containsKey(DbAliases.LOCATION_ADDRESS_2)) {
setAddress2(rs.getString(DbAliases.LOCATION_ADDRESS_2));
}
if (columns.containsKey(DbAliases.LOCATION_CITY)) {
setCity(rs.getString(DbAliases.LOCATION_CITY));
}
if (columns.containsKey(DbAliases.LOCATION_STATE)) {
setState(rs.getString(DbAliases.LOCATION_STATE));
}
if (columns.containsKey(DbAliases.LOCATION_ZIP)) {
setZipCode(rs.getString(DbAliases.LOCATION_ZIP));
}
if (columns.containsKey(DbAliases.LOCATION_COUNTRY)) {
setCountry(rs.getString(DbAliases.LOCATION_COUNTRY));
}
if (columns.containsKey(DbAliases.LOCATION_PHONE)) {
setPhoneNumber(rs.getString(DbAliases.LOCATION_PHONE));
}
} catch (SQLException e) {
ApiFunctions.throwAsRuntimeException(e);
}
}
/** Adds a kc column */
public void addColumnKcData(String cui, String domainObjectType) {
if (ApiFunctions.isEmpty(cui)) {
throw new ApiException("Null cui encountered");
} else if (ApiFunctions.isEmpty(domainObjectType)) {
throw new ApiException("Null domain object type encountered");
} else {
if (TagTypes.DOMAIN_OBJECT_VALUE_SAMPLE.equalsIgnoreCase(domainObjectType)) {
getQuerySampleKcData().addColumn(cui);
} else if (TagTypes.DOMAIN_OBJECT_VALUE_CASE.equalsIgnoreCase(domainObjectType)) {
getQueryConsentKcData().addColumn(cui);
} else if (TagTypes.DOMAIN_OBJECT_VALUE_DONOR.equalsIgnoreCase(domainObjectType)) {
getQueryDonorKcData().addColumn(cui);
} else {
throw new ApiException("Unknown domain object type encountered: " + domainObjectType);
}
}
}
/** @see com.ardais.bigr.library.web.column.SampleColumnImpl#getBodyText(SampleRowParams) */
protected String getBodyText(SampleRowParams rp) throws IOException {
StringBuffer result = new StringBuffer(128);
if (ApiFunctions.safeStringLength(getRawBodyText(rp)) > 0) {
result.append("<td bgColor=red>");
} else {
result.append("<td>");
}
result.append(getRawBodyText(rp));
result.append("</td>");
return result.toString();
}
/**
* Populates this <code>RequestBoxDto</code> from the data in the current row of the result set.
*
* @param columns a <code>Map</code> containing a key for each column in the <code>ResultSet
* </code>. Each key must be one of the column alias constants in {@link
* com.ardais.bigr.util.DbAliases} and the corresponding value is ignored.
* @param rs the <code>ResultSet</code>
*/
public void populate(Map columns, ResultSet rs) {
try {
if (columns.containsKey(DbAliases.REQUEST_BOX_BOX_BARCODE_ID)) {
setBoxId(rs.getString(DbAliases.REQUEST_BOX_BOX_BARCODE_ID));
}
if (columns.containsKey(DbAliases.REQUEST_BOX_SHIPPED_YN)) {
setShipped("Y".equals(rs.getString(DbAliases.REQUEST_BOX_SHIPPED_YN).toUpperCase()));
}
} catch (SQLException e) {
ApiFunctions.throwAsRuntimeException(e);
}
}
private void validatePrinterLabelTemplates(
Account account, LabelPrinter printer, StringBuffer problems, boolean appendComma) {
Map templates = printer.getLabelTemplates();
// if there are no label templates defined for the printer, return an error
if (templates.isEmpty()) {
if (appendComma) {
problems.append(",");
}
problems.append(
" printer with name = "
+ printer.getName()
+ " in account with id = "
+ account.getId()
+ " has no label templates defined.");
appendComma = true;
} else {
Iterator iterator = templates.keySet().iterator();
while (iterator.hasNext()) {
LabelTemplate template = (LabelTemplate) templates.get(iterator.next());
// make sure every template refers to a known template definition
String templateDefinitionName = template.getLabelTemplateDefinitionName();
if (printer
.getParent()
.getLabelTemplateDefinitions()
.get(templateDefinitionName.toLowerCase())
== null) {
if (appendComma) {
problems.append(",");
}
problems.append(
" label template for printer ("
+ printer.getName()
+ ") references an unknown labelTemplateDefinition ("
+ templateDefinitionName
+ ")");
appendComma = true;
}
// make sure every template has a fully qualified name value
String fullName = template.getFullyQualifiedName();
if (ApiFunctions.isEmpty(fullName)) {
if (appendComma) {
problems.append(",");
}
problems.append(
" label template with labelTemplateDefinitionName = "
+ templateDefinitionName
+ " has no fully qualified name value");
appendComma = true;
}
}
}
}
/**
* Creates a new <code>PathReportSectionData</code>, initialized from the data in the
* PathReportSectionData passed in.
*
* @param pathReportSectionData the <code>PathReportSectionData</code>
*/
public PathReportSectionData(PathReportSectionData pathReportSectionData) {
this();
BigrBeanUtilsBean.SINGLETON.copyProperties(this, pathReportSectionData);
// any mutable objects must be handled seperately (BigrBeanUtilsBean.copyProperties
// does a shallow copy.
if (!ApiFunctions.isEmpty(pathReportSectionData.getFindings())) {
_findings.clear();
Iterator iterator = pathReportSectionData.getFindings().iterator();
while (iterator.hasNext()) {
_findings.add(
new PathReportSectionFindingData((PathReportSectionFindingData) iterator.next()));
}
}
}
/**
* Insert the method's description here. Creation date: (2/8/2001 6:51:19 PM)
*
* @param myError java.lang.String
*/
private void retry(String myError) throws Exception {
// Get the security info.
SecurityInfo securityInfo = WebUtils.getSecurityInfo(request);
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.
BoxScanData bsd = BoxLayoutUtils.prepareForBoxScan(securityInfo);
boxLayoutId = bsd.getDefaultBoxLayoutId();
}
}
BoxLayoutDto boxLayoutDto = BoxLayoutUtils.getBoxLayoutDto(boxLayoutId);
request.setAttribute("boxLayoutDto", boxLayoutDto);
retry(myError, RETRY_PATH);
}
/** 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;
}
private void validateAccountLabelPrinters(Account account, StringBuffer problems) {
boolean appendComma = problems.length() > 0;
Map printers = account.getLabelPrinters();
// if there are no label printers defined for the account, return an error
if (printers.isEmpty()) {
if (appendComma) {
problems.append(",");
}
problems.append(" account with id = " + account.getId() + " has no printers defined.");
appendComma = true;
} else {
Map displayNames = new HashMap();
Iterator iterator = printers.keySet().iterator();
while (iterator.hasNext()) {
LabelPrinter printer = (LabelPrinter) printers.get(iterator.next());
String name = printer.getName();
// check that the name by which the printer will be displayed (display name if present,
// otherwise name) is unique
String displayName = printer.getDisplayName();
if (ApiFunctions.isEmpty(displayName)) {
displayName = name;
}
if (displayNames.put(displayName, displayName) != null) {
if (appendComma) {
problems.append(",");
}
problems.append(
" printer with name = "
+ name
+ " has the same display name as another printer in the account");
appendComma = true;
}
// make sure the printer is set up for at least one type of printing mechanism
// (i.e. tcp/ip, email, etc)
if (!printer.isEmailBasedPrintingEnabled()
&& !printer.isFileBasedPrintingEnabled()
&& !printer.isTcpIpBasedPrintingEnabled()) {
if (appendComma) {
problems.append(",");
}
problems.append(" printer with name = " + name + " has no printing mechanism enabled");
appendComma = true;
}
// make sure all required printing information has been specified
else {
if (printer.isEmailBasedPrintingEnabled()) {
if (ApiFunctions.isEmpty(printer.getEmailAddress())) {
if (appendComma) {
problems.append(",");
}
problems.append(" printer with name = " + name + " has no email address.");
appendComma = true;
}
if (ApiFunctions.isEmpty(printer.getEmailSubject())) {
if (appendComma) {
problems.append(",");
}
problems.append(" printer with name = " + name + " has no email subject.");
appendComma = true;
}
}
if (printer.isFileBasedPrintingEnabled()) {
if (!ApiFunctions.isEmpty(printer.getFileTransferCommand())
&& printer
.getFileTransferCommand()
.indexOf(Constants.LABEL_PRINTING_TRANSFER_COMMAND_FILE_INSERTION_STRING)
< 0) {
if (appendComma) {
problems.append(",");
}
problems.append(
" printer with name = "
+ name
+ " has a file transfer command with no insertion point for the filename.");
appendComma = true;
}
if (ApiFunctions.isEmpty(printer.getFileName())) {
if (appendComma) {
problems.append(",");
}
problems.append(" printer with name = " + name + " has no file name.");
appendComma = true;
}
if (ApiFunctions.isEmpty(printer.getFileExtension())) {
if (appendComma) {
problems.append(",");
}
problems.append(" printer with name = " + name + " has no file extension.");
appendComma = true;
}
}
if (printer.isTcpIpBasedPrintingEnabled()) {
if (ApiFunctions.isEmpty(printer.getTcpIpHost())) {
if (appendComma) {
problems.append(",");
}
problems.append(" printer with name = " + name + " has no tcp/ip host.");
appendComma = true;
}
String tcpIpPort = printer.getTcpIpPort();
if (ApiFunctions.isEmpty(tcpIpPort)) {
if (appendComma) {
problems.append(",");
}
problems.append(" printer with name = " + name + " has no tcp/ip port.");
appendComma = true;
} else {
if (!ApiFunctions.isInteger(tcpIpPort)) {
if (appendComma) {
problems.append(",");
}
problems.append(" printer with name = " + name + " has an invalid tcp/ip port.");
appendComma = true;
}
}
}
}
// validate the label templates specified as available on this printer
validatePrinterLabelTemplates(account, printer, problems, appendComma);
}
}
}
/**
* Creates a new <code>PathReportSectionData</code>, initialized from the data in the current row
* of the result set.
*/
public PathReportSectionData(ResultSet rs) {
this();
try {
ResultSetMetaData meta = rs.getMetaData();
int columnCount = meta.getColumnCount();
HashMap lookup = new HashMap();
for (int i = 0; i < columnCount; i++) {
lookup.put(meta.getColumnName(i + 1).toLowerCase(), null);
}
if (lookup.containsKey("cell_infiltrate_amt"))
setCellInfiltrateAmount(rs.getString("cell_infiltrate_amt"));
if (lookup.containsKey("consent_id")) setConsentId(rs.getString("consent_id"));
if (lookup.containsKey("create_user")) setCreateUser(rs.getString("create_user"));
if (lookup.containsKey("diagnosis_concept_id"))
setDiagnosis(rs.getString("diagnosis_concept_id"));
if (lookup.containsKey("distant_metastasis"))
setDistantMetastasis(rs.getString("distant_metastasis"));
if (lookup.containsKey("distant_metastasis_ind"))
setDistantMetastasisInd(rs.getString("distant_metastasis_ind"));
if (lookup.containsKey("extensive_intraductal_comp"))
setExtensiveIntraductalComp(rs.getString("extensive_intraductal_comp"));
if (lookup.containsKey("extranodal_spread"))
setExtranodalSpread(rs.getString("extranodal_spread"));
if (lookup.containsKey("histological_nuclear_grade"))
setHistologicalNuclearGrade(rs.getString("histological_nuclear_grade"));
if (lookup.containsKey("histological_type"))
setHistologicalType(rs.getString("histological_type"));
if (lookup.containsKey("inflamm_cell_infiltrate"))
setInflammCellInfiltrate(rs.getString("inflamm_cell_infiltrate"));
if (lookup.containsKey("joint_component")) setJointComponent(rs.getString("joint_component"));
if (lookup.containsKey("last_update_user"))
setLastUpdateUser(rs.getString("last_update_user"));
if (lookup.containsKey("lymph_node_notes"))
setLymphNodeNotes(rs.getString("lymph_node_notes"));
if (lookup.containsKey("lymph_node_stage"))
setLymphNodeStage(rs.getString("lymph_node_stage"));
if (lookup.containsKey("lymph_node_stage_ind"))
setLymphNodeStageInd(rs.getString("lymph_node_stage_ind"));
if (lookup.containsKey("lymphatic_vascular_invasion"))
setLymphaticVascularInvasion(rs.getString("lymphatic_vascular_invasion"));
if (lookup.containsKey("margins_involved_desc"))
setMarginsInvolved(rs.getString("margins_involved_desc"));
if (lookup.containsKey("margins_uninvolved_desc"))
setMarginsUninvolved(rs.getString("margins_uninvolved_desc"));
if (lookup.containsKey("other_distant_metastasis"))
setDistantMetastasisOther(rs.getString("other_distant_metastasis"));
if (lookup.containsKey("other_dx_name")) setDiagnosisOther(rs.getString("other_dx_name"));
if (lookup.containsKey("other_finding_tc_name"))
setTissueFindingOther(rs.getString("other_finding_tc_name"));
if (lookup.containsKey("other_histo_nuclear_grade"))
setHistologicalNuclearGradeOther(rs.getString("other_histo_nuclear_grade"));
if (lookup.containsKey("other_histological_type"))
setHistologicalTypeOther(rs.getString("other_histological_type"));
if (lookup.containsKey("other_lymph_node_stage"))
setLymphNodeStageOther(rs.getString("other_lymph_node_stage"));
if (lookup.containsKey("other_origin_tc_name"))
setTissueOriginOther(rs.getString("other_origin_tc_name"));
if (lookup.containsKey("other_stage_grouping"))
setStageGroupingOther(rs.getString("other_stage_grouping"));
if (lookup.containsKey("other_tumor_stage_desc"))
setTumorStageDescOther(rs.getString("other_tumor_stage_desc"));
if (lookup.containsKey("other_tumor_stage_type"))
setTumorStageTypeOther(rs.getString("other_tumor_stage_type"));
if (lookup.containsKey("path_report_id")) setPathReportId(rs.getString("path_report_id"));
if (lookup.containsKey("path_report_section_id"))
setPathReportSectionId(rs.getString("path_report_section_id"));
if (lookup.containsKey("path_section_notes"))
setSectionNotes(ApiFunctions.getStringFromClob(rs.getClob("path_section_notes")));
if (lookup.containsKey("perineural_invasion_ind"))
setPerineuralInvasion(rs.getString("perineural_invasion_ind"));
if (lookup.containsKey("primary_gleason_score")) {
String score = rs.getString("primary_gleason_score");
if (score != null) setGleasonPrimary(new Integer(score));
}
if (lookup.containsKey("primary_ind")) setPrimary(rs.getString("primary_ind"));
if (lookup.containsKey("secondary_gleason_score")) {
String score = rs.getString("secondary_gleason_score");
if (score != null) setGleasonSecondary(new Integer(score));
}
if (lookup.containsKey("section_identifier"))
setSectionIdentifier(rs.getString("section_identifier"));
if (lookup.containsKey("size_largest_nodal_mets"))
setSizeLargestNodalMets(rs.getString("size_largest_nodal_mets"));
if (lookup.containsKey("stage_grouping")) setStageGrouping(rs.getString("stage_grouping"));
if (lookup.containsKey("tissue_finding_concept_id"))
setTissueFinding(rs.getString("tissue_finding_concept_id"));
if (lookup.containsKey("tissue_origin_concept_id"))
setTissueOrigin(rs.getString("tissue_origin_concept_id"));
if (lookup.containsKey("total_gleason_score")) {
String score = rs.getString("total_gleason_score");
if (score != null) setGleasonTotal(new Integer(score));
}
if (lookup.containsKey("total_nodes_examined"))
setTotalNodesExamined(rs.getString("total_nodes_examined"));
if (lookup.containsKey("total_nodes_positive"))
setTotalNodesPositive(rs.getString("total_nodes_positive"));
if (lookup.containsKey("tumor_configuration"))
setTumorConfiguration(rs.getString("tumor_configuration"));
if (lookup.containsKey("tumor_size")) setTumorSize(rs.getString("tumor_size"));
if (lookup.containsKey("tumor_stage_desc"))
setTumorStageDesc(rs.getString("tumor_stage_desc"));
if (lookup.containsKey("tumor_stage_desc_ind"))
setTumorStageDescInd(rs.getString("tumor_stage_desc_ind"));
if (lookup.containsKey("tumor_stage_type"))
setTumorStageType(rs.getString("tumor_stage_type"));
if (lookup.containsKey("tumor_weight")) setTumorWeight(rs.getString("tumor_weight"));
if (lookup.containsKey("venous_vessel_invasion"))
setVenousVesselInvasion(rs.getString("venous_vessel_invasion"));
} catch (SQLException e) {
throw new ApiException(e);
}
}
private void validateAccount(Account account, StringBuffer problems) {
boolean appendComma = problems.length() > 0;
// validate the account id exists and is a known account id
String id = ApiFunctions.safeTrim(account.getId());
if (ApiFunctions.isEmpty(id)) {
if (appendComma) {
problems.append(",");
}
problems.append(" account with empty id encountered");
appendComma = true;
} else {
ArdaisaccountAccessBean ardaisAccount = null;
try {
ardaisAccount = new ArdaisaccountAccessBean(new ArdaisaccountKey(id));
} catch (Exception e) {
if (appendComma) {
problems.append(",");
}
problems.append(" account with unknown id (" + id + ") encountered");
appendComma = true;
}
}
// validate that the bartender command line exists and has the correct insertion points
String bartenderCommandLine = account.getBartenderCommandLine();
if (ApiFunctions.isEmpty(bartenderCommandLine)) {
if (appendComma) {
problems.append(",");
}
problems.append(" account with empty bartenderCommandLine encountered.");
appendComma = true;
} else {
if (bartenderCommandLine.indexOf(Constants.LABEL_PRINTING_INSERTION_STRING_LABEL_PRINTER)
<= 0) {
if (appendComma) {
problems.append(",");
}
problems.append(
" account with bartenderCommandLine having no printer insertion string encountered.");
appendComma = true;
}
if (bartenderCommandLine.indexOf(Constants.LABEL_PRINTING_INSERTION_STRING_LABEL_TEMPLATE)
<= 0) {
if (appendComma) {
problems.append(",");
}
problems.append(
" account with bartenderCommandLine having no template insertion string encountered.");
appendComma = true;
}
}
// validate the results form definitions in the account
validateAccountResultsFormDefinitions(account, problems);
// validate the label template definitions in the account
validateAccountLabelTemplateDefinitions(account, problems);
// validate the label printers in the account
validateAccountLabelPrinters(account, problems);
}
/**
* Populates this <code>PathReportSectionData</code> from the data in the current row of the
* result set.
*
* @param columns a <code>Map</code> containing a key for each column in the <code>ResultSet
* </code>. Each key must be one of the column alias constants in {@link
* com.ardais.bigr.util.DbAliases} and the corresponding value is ignored.
* @param rs the <code>ResultSet</code>
*/
public void populate(Map columns, ResultSet rs) {
try {
if (columns.containsKey(DbAliases.SECTION_DX)) {
setDiagnosis(rs.getString(DbAliases.SECTION_DX));
}
if (columns.containsKey(DbAliases.SECTION_DX_OTHER)) {
setDiagnosisOther(rs.getString(DbAliases.SECTION_DX_OTHER));
}
if (columns.containsKey(DbAliases.SECTION_HNG)) {
setHistologicalNuclearGrade(rs.getString(DbAliases.SECTION_HNG));
}
if (columns.containsKey(DbAliases.SECTION_ID)) {
setPathReportSectionId(rs.getString(DbAliases.SECTION_ID));
}
if (columns.containsKey(DbAliases.SECTION_GLEASON_PRIMARY)) {
if (rs.getString(DbAliases.SECTION_GLEASON_PRIMARY) != null) {
setGleasonPrimary(new Integer(rs.getInt(DbAliases.SECTION_GLEASON_PRIMARY)));
}
}
if (columns.containsKey(DbAliases.SECTION_GLEASON_SECONDARY)) {
if (rs.getString(DbAliases.SECTION_GLEASON_SECONDARY) != null) {
setGleasonSecondary(new Integer(rs.getInt(DbAliases.SECTION_GLEASON_SECONDARY)));
}
}
if (columns.containsKey(DbAliases.SECTION_GLEASON_TOTAL)) {
if (rs.getString(DbAliases.SECTION_GLEASON_TOTAL) != null) {
setGleasonTotal(new Integer(rs.getInt(DbAliases.SECTION_GLEASON_TOTAL)));
}
}
if (columns.containsKey(DbAliases.SECTION_LYMPH_STAGE)) {
setLymphNodeStage(rs.getString(DbAliases.SECTION_LYMPH_STAGE));
}
if (columns.containsKey(DbAliases.SECTION_METASTASIS)) {
setDistantMetastasis(rs.getString(DbAliases.SECTION_METASTASIS));
}
if (columns.containsKey(DbAliases.SECTION_STAGE_GROUPING)) {
setStageGrouping(rs.getString(DbAliases.SECTION_STAGE_GROUPING));
}
if (columns.containsKey(DbAliases.SECTION_TISSUE_FINDING)) {
setTissueFinding(rs.getString(DbAliases.SECTION_TISSUE_FINDING));
}
if (columns.containsKey(DbAliases.SECTION_TISSUE_FINDING_OTHER)) {
setTissueFindingOther(rs.getString(DbAliases.SECTION_TISSUE_FINDING_OTHER));
}
if (columns.containsKey(DbAliases.SECTION_TISSUE_ORIGIN)) {
setTissueOrigin(rs.getString(DbAliases.SECTION_TISSUE_ORIGIN));
}
if (columns.containsKey(DbAliases.SECTION_TISSUE_ORIGIN_OTHER)) {
setTissueOriginOther(rs.getString(DbAliases.SECTION_TISSUE_ORIGIN_OTHER));
}
if (columns.containsKey(DbAliases.SECTION_TUMOR_STAGE)) {
setTumorStageDesc(rs.getString(DbAliases.SECTION_TUMOR_STAGE));
}
if (columns.containsKey(DbAliases.SECTION_TUMOR_STAGE_TYPE)) {
setTumorStageType(rs.getString(DbAliases.SECTION_TUMOR_STAGE_TYPE));
}
if (columns.containsKey(DbAliases.SECTION_PRIMARY_IND)) {
setPrimary(rs.getString(DbAliases.SECTION_PRIMARY_IND));
}
if (columns.containsKey(DbAliases.SECTION_PATH_REPORT_ID)) {
setPathReportId(rs.getString(DbAliases.SECTION_PATH_REPORT_ID));
}
if (columns.containsKey(DbAliases.SECTION_TUMOR_SIZE)) {
setTumorSize(rs.getString(DbAliases.SECTION_TUMOR_SIZE));
}
if (columns.containsKey(DbAliases.SECTION_TUMOR_WEIGHT)) {
setTumorWeight(rs.getString(DbAliases.SECTION_TUMOR_WEIGHT));
}
} catch (SQLException e) {
ApiFunctions.throwAsRuntimeException(e);
}
}
/* (non-Javadoc)
* @see com.ardais.bigr.btx.framework.DescribableAsHistoryObject#describeAsHistoryObject()
*/
public Object describeAsHistoryObject() {
BtxHistoryAttributes attributes = new BtxHistoryAttributes();
if (!ApiFunctions.isEmpty(getConsentId())) {
attributes.setAttribute("consentId", getConsentId());
}
if (!ApiFunctions.isEmpty(getCellInfiltrateAmount())) {
attributes.setAttribute(
"cellInfiltrateAmount",
GbossFactory.getInstance().getDescription(getCellInfiltrateAmount()));
}
if (!ApiFunctions.isEmpty(getDiagnosis())) {
attributes.setAttribute("diagnosis", BigrGbossData.getDiagnosisDescription(getDiagnosis()));
}
if (!ApiFunctions.isEmpty(getDiagnosisOther())) {
attributes.setAttribute("diagnosisOther", getDiagnosisOther());
}
if (!ApiFunctions.isEmpty(getDistantMetastasis())) {
attributes.setAttribute(
"distantMetastasis", GbossFactory.getInstance().getDescription(getDistantMetastasis()));
}
if (!ApiFunctions.isEmpty(getDistantMetastasisInd())) {
attributes.setAttribute("distantMetastasisInd", getDistantMetastasisInd());
}
if (!ApiFunctions.isEmpty(getDistantMetastasisOther())) {
attributes.setAttribute("distantMetastasisOther", getDistantMetastasisOther());
}
if (!ApiFunctions.isEmpty(getExtensiveIntraductalComp())) {
attributes.setAttribute(
"extensiveIntraductalComp",
GbossFactory.getInstance().getDescription(getExtensiveIntraductalComp()));
}
if (!ApiFunctions.isEmpty(getExtranodalSpread())) {
attributes.setAttribute(
"extranodalSpread", GbossFactory.getInstance().getDescription(getExtranodalSpread()));
}
if (getGleasonPrimary() != null && !ApiFunctions.isEmpty(getGleasonPrimary().toString())) {
attributes.setAttribute("gleasonPrimary", getGleasonPrimary().toString());
}
if (getGleasonSecondary() != null && !ApiFunctions.isEmpty(getGleasonSecondary().toString())) {
attributes.setAttribute("gleasonSecondary", getGleasonSecondary().toString());
}
if (getGleasonTotal() != null && !ApiFunctions.isEmpty(getGleasonTotal().toString())) {
attributes.setAttribute("gleasonTotal", getGleasonTotal().toString());
}
if (!ApiFunctions.isEmpty(getHistologicalNuclearGrade())) {
attributes.setAttribute(
"histologicalNuclearGrade",
GbossFactory.getInstance().getDescription(getHistologicalNuclearGrade()));
}
if (!ApiFunctions.isEmpty(getHistologicalNuclearGradeOther())) {
attributes.setAttribute("histologicalNuclearGradeOther", getHistologicalNuclearGradeOther());
}
if (!ApiFunctions.isEmpty(getHistologicalType())) {
attributes.setAttribute(
"histologicalType", GbossFactory.getInstance().getDescription(getHistologicalType()));
}
if (!ApiFunctions.isEmpty(getHistologicalTypeOther())) {
attributes.setAttribute("histologicalTypeOther", getHistologicalTypeOther());
}
if (!ApiFunctions.isEmpty(getInflammCellInfiltrate())) {
attributes.setAttribute(
"inflammCellInfiltrate",
GbossFactory.getInstance().getDescription(getInflammCellInfiltrate()));
}
if (!ApiFunctions.isEmpty(getJointComponent())) {
attributes.setAttribute(
"jointComponent", GbossFactory.getInstance().getDescription(getJointComponent()));
}
if (!ApiFunctions.isEmpty(getLymphaticVascularInvasion())) {
attributes.setAttribute(
"lymphaticVascularInvasion",
GbossFactory.getInstance().getDescription(getLymphaticVascularInvasion()));
}
if (!ApiFunctions.isEmpty(getLymphNodeNotes())) {
attributes.setAttribute("lymphNodeNotes", getLymphNodeNotes());
}
if (!ApiFunctions.isEmpty(getLymphNodeStage())) {
attributes.setAttribute(
"lymphNodeStage", GbossFactory.getInstance().getDescription(getLymphNodeStage()));
}
if (!ApiFunctions.isEmpty(getLymphNodeStageOther())) {
attributes.setAttribute("lymphNodeStageOther", getLymphNodeStageOther());
}
if (!ApiFunctions.isEmpty(getLymphNodeStageInd())) {
attributes.setAttribute("lymphNodeStageInd", getLymphNodeStageInd());
}
if (!ApiFunctions.isEmpty(getMarginsInvolved())) {
attributes.setAttribute("marginsInvolved", getMarginsInvolved());
}
if (!ApiFunctions.isEmpty(getMarginsUninvolved())) {
attributes.setAttribute("marginsUninvolved", getMarginsUninvolved());
}
if (!ApiFunctions.isEmpty(getPerineuralInvasion())) {
attributes.setAttribute(
"perineuralInvasion", GbossFactory.getInstance().getDescription(getPerineuralInvasion()));
}
if (!ApiFunctions.isEmpty(getPrimary())) {
attributes.setAttribute("primary", getPrimary());
}
if (!ApiFunctions.isEmpty(getSectionIdentifier())) {
attributes.setAttribute(
"sectionIdentifier", GbossFactory.getInstance().getDescription(getSectionIdentifier()));
}
if (!ApiFunctions.isEmpty(getSectionNotes())) {
attributes.setAttribute("sectionNotes", getSectionNotes());
}
if (!ApiFunctions.isEmpty(getSizeLargestNodalMets())) {
attributes.setAttribute("sizeLargestNodalMets", getSizeLargestNodalMets());
}
if (!ApiFunctions.isEmpty(getStageGrouping())) {
attributes.setAttribute(
"stageGrouping", GbossFactory.getInstance().getDescription(getStageGrouping()));
}
if (!ApiFunctions.isEmpty(getStageGroupingOther())) {
attributes.setAttribute("stageGroupingOther", getStageGroupingOther());
}
if (!ApiFunctions.isEmpty(getTissueFinding())) {
attributes.setAttribute(
"tissueFinding", BigrGbossData.getTissueDescription(getTissueFinding()));
}
if (!ApiFunctions.isEmpty(getTissueFindingOther())) {
attributes.setAttribute("tissueFindingOther", getTissueFindingOther());
}
if (!ApiFunctions.isEmpty(getTissueOrigin())) {
attributes.setAttribute(
"tissueOrigin", BigrGbossData.getTissueDescription(getTissueOrigin()));
}
if (!ApiFunctions.isEmpty(getTissueOriginOther())) {
attributes.setAttribute("tissueOriginOther", getTissueOriginOther());
}
if (!ApiFunctions.isEmpty(getTotalNodesExamined())) {
attributes.setAttribute(
"totalNodesExamined", GbossFactory.getInstance().getDescription(getTotalNodesExamined()));
}
if (!ApiFunctions.isEmpty(getTotalNodesPositive())) {
attributes.setAttribute(
"totalNodesPositive", GbossFactory.getInstance().getDescription(getTotalNodesPositive()));
}
if (!ApiFunctions.isEmpty(getTumorConfig())) {
attributes.setAttribute(
"tumorConfig", GbossFactory.getInstance().getDescription(getTumorConfig()));
}
if (!ApiFunctions.isEmpty(getTumorSize())) {
attributes.setAttribute("tumorSize", getTumorSize());
}
if (!ApiFunctions.isEmpty(getTumorStageDesc())) {
attributes.setAttribute(
"tumorStageDesc", GbossFactory.getInstance().getDescription(getTumorStageDesc()));
}
if (!ApiFunctions.isEmpty(getTumorStageDescInd())) {
attributes.setAttribute("tumorStageDescInd", getTumorStageDescInd());
}
if (!ApiFunctions.isEmpty(getTumorStageDescOther())) {
attributes.setAttribute("tumorStageDescOther", getTumorStageDescOther());
}
if (!ApiFunctions.isEmpty(getTumorStageType())) {
attributes.setAttribute(
"tumorStageType", GbossFactory.getInstance().getDescription(getTumorStageType()));
}
if (!ApiFunctions.isEmpty(getTumorStageTypeOther())) {
attributes.setAttribute("tumorStageTypeOther", getTumorStageTypeOther());
}
if (!ApiFunctions.isEmpty(getTumorWeight())) {
attributes.setAttribute("tumorWeight", getTumorWeight());
}
if (!ApiFunctions.isEmpty(getVenousVesselInvasion())) {
attributes.setAttribute(
"venousVesselInvasion",
GbossFactory.getInstance().getDescription(getVenousVesselInvasion()));
}
return attributes;
}
/**
* Populates the full details of the tissue sample data beans specified in the input <code>Map
* </code>. One or more columns must be specified before calling this method. The only filters are
* the sample IDs that are specified in the <code>Map</code>.
*
* @param sampleDataBeans a <code>Map</code> of {@link com.ardais.bigr.javabeans.SampleData} data
* beans, keyed by the ids of the samples
*/
public void getDetails(Map sampleDataBeans) {
if (sampleDataBeans.isEmpty()) {
return;
}
long tStart = 0;
String myClassName = null;
if (_perfLog.isDebugEnabled()) {
myClassName = ApiFunctions.shortClassName(getClass().getName());
_perfLog.debug(" C: START " + myClassName + ".getDetails");
tStart = System.currentTimeMillis();
}
// Create the Maps that will hold the parent data beans.
Map asmMap = new HashMap();
Map consentMap = new HashMap();
Map donorMap = new HashMap();
// Iterate over all queries.
Iterator queries = _queries.entrySet().iterator();
while (queries.hasNext()) {
long tLoopStart = System.currentTimeMillis();
Map.Entry entry = (Map.Entry) queries.next();
String queryKey = (String) entry.getKey();
if (queryKey.equals(KEY_SAMPLE)) {
TissueDetailQueryBuilder query = (TissueDetailQueryBuilder) entry.getValue();
query.getDetails(sampleDataBeans);
asmMap = query.getAsmData();
} else if (queryKey.equals(KEY_LIMS)) {
PathologyEvaluationDetailQueryBuilder query =
(PathologyEvaluationDetailQueryBuilder) entry.getValue();
query.getDetailsForSamples(sampleDataBeans);
} else if (queryKey.equals(KEY_IMAGES)) {
ImageDetailQueryBuilder query = (ImageDetailQueryBuilder) entry.getValue();
query.getDetailsForSamples(sampleDataBeans);
} else if (queryKey.equals(KEY_PROJECT)) {
ProjectDetailQueryBuilder query = (ProjectDetailQueryBuilder) entry.getValue();
query.getDetailsForSamples(sampleDataBeans);
} else if (queryKey.equals(KEY_ORDER)) {
OrderDetailQueryBuilder query = (OrderDetailQueryBuilder) entry.getValue();
query.getDetailsForSamples(sampleDataBeans);
} else if (queryKey.equals(KEY_SHOPPING_CART)) {
ShoppingCartDetailQueryBuilder query = (ShoppingCartDetailQueryBuilder) entry.getValue();
query.getDetailsForSamples(sampleDataBeans);
} else if (queryKey.equals(KEY_ASM)) {
AsmDetailQueryBuilder query = (AsmDetailQueryBuilder) entry.getValue();
query.getDetails(asmMap);
consentMap = query.getConsentData();
} else if (queryKey.equals(KEY_CONSENT)) {
ConsentDetailQueryBuilder query = (ConsentDetailQueryBuilder) entry.getValue();
query.getDetails(consentMap);
donorMap = query.getDonorData();
} else if (queryKey.equals(KEY_DONOR)) {
DonorDetailQueryBuilder query = (DonorDetailQueryBuilder) entry.getValue();
query.getDetails(donorMap);
} else if (queryKey.equals(KEY_PATH)) {
PathologyReportDetailQueryBuilder query =
(PathologyReportDetailQueryBuilder) entry.getValue();
query.getDetailsForConsents(consentMap);
} else if (queryKey.equals(KEY_LOGICAL_REPOSITORY)) {
LogicalRepositoryDetailQueryBuilder query =
(LogicalRepositoryDetailQueryBuilder) entry.getValue();
query.getDetails(sampleDataBeans);
} else if (queryKey.equals(KEY_SAMPLE_LOCATION)) {
SampleLocationDetailQueryBuilder query =
(SampleLocationDetailQueryBuilder) entry.getValue();
query.getDetails(sampleDataBeans);
} else if (queryKey.equals(KEY_DIAGNOSTIC)) {
DiagnosticTestDetailQueryBuilder query =
(DiagnosticTestDetailQueryBuilder) entry.getValue();
query.getDetailsForConsents(consentMap);
} else if (queryKey.equals(KEY_SAMPLE_KC)) {
KcDetailQueryBuilder query = (KcDetailQueryBuilder) entry.getValue();
query.getDetails(sampleDataBeans);
} else if (queryKey.equals(KEY_CONSENT_KC)) {
KcDetailQueryBuilder query = (KcDetailQueryBuilder) entry.getValue();
query.getDetails(consentMap);
} else if (queryKey.equals(KEY_DONOR_KC)) {
KcDetailQueryBuilder query = (KcDetailQueryBuilder) entry.getValue();
query.getDetails(donorMap);
} else {
throw new ApiException(
"Unrecognized query key in ProductDetailQueryBuilder.getDetails:" + queryKey);
}
if (_perfLog.isDebugEnabled()) {
long elapsedTime = System.currentTimeMillis() - tLoopStart;
_perfLog.debug(" D: do detail query " + queryKey + " (" + elapsedTime + " ms)");
}
} // while next query
if (_perfLog.isDebugEnabled()) {
long elapsedTime = System.currentTimeMillis() - tStart;
_perfLog.debug(" C: END " + myClassName + ".getDetails" + " (" + elapsedTime + " ms)");
}
}
private void validateAccountLabelTemplateDefinitions(Account account, StringBuffer problems) {
boolean appendComma = problems.length() > 0;
Map templateDefinitions = account.getLabelTemplateDefinitions();
// if there are no label template definitions defined for the account, return an error
if (templateDefinitions.isEmpty()) {
if (appendComma) {
problems.append(",");
}
problems.append(
" account with id = " + account.getId() + " has no label template definitions defined.");
appendComma = true;
} else {
Map displayNames = new HashMap();
Iterator iterator = templateDefinitions.keySet().iterator();
while (iterator.hasNext()) {
LabelTemplateDefinition templateDefinition =
(LabelTemplateDefinition) templateDefinitions.get(iterator.next());
String name = templateDefinition.getName();
// check that the name by which the template will be displayed (display name if present,
// otherwise name) is unique
String displayName = templateDefinition.getDisplayName();
if (ApiFunctions.isEmpty(displayName)) {
displayName = name;
}
if (displayNames.put(displayName, displayName) != null) {
if (appendComma) {
problems.append(",");
}
problems.append(
" label template definition with name = "
+ name
+ " has the same display name as another template definition in the account");
appendComma = true;
}
// check that the object type is valid
String objectType = templateDefinition.getObjectType();
if (ApiFunctions.isEmpty(objectType)) {
if (appendComma) {
problems.append(",");
}
problems.append(
" label template definition with name = " + name + " has an empty object type");
appendComma = true;
} else {
if (Constants.LABEL_PRINTING_OBJECT_TYPES.get(objectType) == null) {
if (appendComma) {
problems.append(",");
}
problems.append(
" label template definition with name = " + name + " has an unknown object type");
appendComma = true;
}
}
// check that the object subtype(s), if present, is/are valid
Collection objectSubtypes = templateDefinition.getObjectSubtypesCollection();
if (!ApiFunctions.isEmpty(objectSubtypes)) {
// currently only sample objects can have a subtype
if (!Constants.LABEL_PRINTING_OBJECT_TYPE_SAMPLE.equalsIgnoreCase(objectType)) {
if (appendComma) {
problems.append(",");
}
problems.append(
" label template definition with name = "
+ name
+ " has object subtype(s) specified but does not have an object type of "
+ Constants.LABEL_PRINTING_OBJECT_TYPE_SAMPLE);
appendComma = true;
}
Iterator subtypeIterator = objectSubtypes.iterator();
while (subtypeIterator.hasNext()) {
String objectSubtype = (String) subtypeIterator.next();
// make sure the subtype(s) is/are valid sample type(s)
if (SystemConfiguration.getSampleType(objectSubtype) == null) {
if (appendComma) {
problems.append(",");
}
problems.append(
" label template definition with name = "
+ name
+ " has an unknown object subtype value of "
+ objectSubtype);
appendComma = true;
}
}
}
// check that the results form definition name is valid
String formDefinitionName = templateDefinition.getResultsFormDefinitionName();
if (ApiFunctions.isEmpty(formDefinitionName)) {
if (appendComma) {
problems.append(",");
}
problems.append(
" label template definition with name = "
+ name
+ " has no results form definition name");
appendComma = true;
} else {
if (templateDefinition
.getParent()
.getResultsFormDefinitions()
.get(formDefinitionName.toLowerCase())
== null) {
if (appendComma) {
problems.append(",");
}
problems.append(
" label template definition with name = "
+ name
+ " references an unknown results form definition name ("
+ formDefinitionName
+ ")");
appendComma = true;
}
}
}
}
}
private String getSessionAttributeQualifiedName(String name) {
String partnerName = getPartnerName();
return (ApiFunctions.isEmpty(partnerName))
? SESSION_ATTRIBUTE_PREFIX + name
: SESSION_ATTRIBUTE_PREFIX + "." + partnerName + "." + name;
}