/**
* This function returns the RoleClass for given attName
*
* @param attName
* @return RoleClass
*/
public static Class getRoleClass(String attName) {
Iterator itr = mappings.iterator();
while (itr.hasNext()) {
ClassRelationshipData crd = (ClassRelationshipData) itr.next();
if (crd.getRoleAttribute().indexOf(attName) != -1) {
return Utility.getClassObject(crd.getRelatedClassName());
}
}
return null;
}
/**
* This method used to set Date values. to prepared statement
*
* @param stmt :TODO
* @param index :
* @param obj :
* @throws SQLException : SQLException
* @throws DAOException : DAOException
*/
protected void setDateColumns(PreparedStatement stmt, int index, Object obj)
throws SQLException, DAOException {
if (obj != null && obj.toString().equals("##")) {
java.util.Date date = null;
try {
date = Utility.parseDate("1-1-9999", "mm-dd-yyyy");
} catch (ParseException exp) {
// TODO have to replace this by parse key
ErrorKey errorKey = ErrorKey.getErrorKey("db.operation.error");
throw new DAOException(errorKey, exp, "HashedDataHandler.java :");
}
Date sqlDate = new Date(date.getTime());
stmt.setDate(index, sqlDate);
}
}
/**
* Returns SimpleConditionsNode if the object named aliasName contains the activityStatus data
* member, else returns null.
*
* @param aliasName The alias name of the object.
* @param className The fully qualified name of the class in which activity status field is to be
* searched.
* @return SimpleConditionsNode if the object named aliasName contains the activityStatus data
* member, else returns null.
*/
private SimpleConditionsNode getActivityStatusCondition(String aliasName, String className)
throws DAOException, ClassNotFoundException {
SimpleConditionsNode activityStatusCondition = null;
if (className.equals(Constants.REPORTED_PROBLEM_CLASS_NAME)) {
return null;
}
// Returns the Class object if it is a valid class else returns null.
Class classObject = edu.wustl.common.util.Utility.getClassObject(className);
if (classObject != null) {
Field[] objectFields = classObject.getDeclaredFields();
for (int i = 0; i < objectFields.length; i++) {
if (objectFields[i].getName().equals(Constants.ACTIVITY_STATUS)) {
activityStatusCondition = new SimpleConditionsNode();
activityStatusCondition.getCondition().getDataElement().setTableName(aliasName);
activityStatusCondition
.getCondition()
.getDataElement()
.setField(Constants.ACTIVITY_STATUS_COLUMN);
activityStatusCondition.getCondition().getOperator().setOperator("!=");
activityStatusCondition.getCondition().setValue(Constants.ACTIVITY_STATUS_DISABLED);
activityStatusCondition
.getCondition()
.getDataElement()
.setFieldType(Constants.FIELD_TYPE_VARCHAR);
return activityStatusCondition;
}
}
Class superClass = classObject.getSuperclass();
if ((activityStatusCondition == null)
&& (superClass.getName().equals("edu.wustl.common.domain.AbstractDomainObject")
== false)) {
String superClassAliasName = getAliasName(superClass);
activityStatusCondition =
getActivityStatusCondition(superClassAliasName, superClass.getName());
}
}
return activityStatusCondition;
}
/**
* @see
* edu.common.dynamicextensions.validation.ValidatorRuleInterface#validate(edu.common.dynamicextensions.domaininterface.AttributeInterface,
* java.lang.Object, java.util.Map)
* @throws DynamicExtensionsValidationException
*/
public boolean validate(
AttributeInterface attribute, Object valueObject, Map<String, String> parameterMap)
throws DynamicExtensionsValidationException {
boolean valid = false;
String attributeName = attribute.getName();
AttributeTypeInformationInterface attributeTypeInformation =
attribute.getAttributeTypeInformation();
if (((valueObject != null) && (!((String) valueObject).trim().equals("")))
&& ((attributeTypeInformation != null)
&& (attributeTypeInformation instanceof DateAttributeTypeInformation))) {
DateAttributeTypeInformation dateAttributeTypeInformation =
(DateAttributeTypeInformation) attributeTypeInformation;
String dateFormat = dateAttributeTypeInformation.getFormat();
String value = (String) valueObject;
if (dateFormat.equals(ProcessorConstants.MONTH_YEAR_FORMAT)) {
value = DynamicExtensionsUtility.formatMonthAndYearDate(value);
value = value.substring(0, value.length() - 4);
}
if (dateFormat.equals(ProcessorConstants.YEAR_ONLY_FORMAT)) {
value = DynamicExtensionsUtility.formatYearDate(value);
value = value.substring(0, value.length() - 4);
}
try {
Date date = null;
date = Utility.parseDate(value, "MM-dd-yyyy");
if (date != null) {
valid = true;
}
} catch (ParseException parseException) {
List<String> placeHolders = new ArrayList<String>();
placeHolders.add(attributeName);
placeHolders.add(dateFormat);
throw new DynamicExtensionsValidationException(
"Validation failed", null, "dynExtn.validation.Date", placeHolders);
}
}
return valid;
}
private void createSCGUnderCPHavingScientistAsPI() {
try {
CollectionProtocol cp = new CollectionProtocol();
cp.setId(new Long(BizTestCaseUtility.CP_WITH_SCIENTIST_AS_PI));
Participant participant = BaseTestCaseUtility.initParticipant();
participant.setSocialSecurityNumber("111-22-3233");
try {
participant.setBirthDate(
Utility.parseDate("05-02-1984", CommonServiceLocator.getInstance().getDatePattern()));
} catch (ParseException e) {
Logger.out.debug("" + e);
}
System.out.println("Participant" + participant);
SessionDataBean bean = (SessionDataBean) getSession().getAttribute("sessionData");
try {
participant = (Participant) appService.createObject(participant);
} catch (Exception e) {
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
BizTestCaseUtility.setNameObjectMap("ParticipantWithScientistAsPI", participant);
CollectionProtocolRegistration collectionProtocolRegistration =
new CollectionProtocolRegistration();
collectionProtocolRegistration.setCollectionProtocol(cp);
collectionProtocolRegistration.setParticipant(participant);
collectionProtocolRegistration.setProtocolParticipantIdentifier("");
collectionProtocolRegistration.setActivityStatus("Active");
try {
collectionProtocolRegistration.setRegistrationDate(
Utility.parseDate("08/15/2006", Utility.datePattern("08/15/2006")));
collectionProtocolRegistration.setConsentSignatureDate(
Utility.parseDate("11/23/2006", Utility.datePattern("11/23/2006")));
System.out.println("Creating CPR");
} catch (ParseException e) {
e.printStackTrace();
}
collectionProtocolRegistration.setSignedConsentDocumentURL("F:/doc/consentDoc.doc");
User user = new User();
user.setId(new Long(1));
collectionProtocolRegistration.setConsentWitness(user);
// Collection consentTierResponseCollection = new LinkedHashSet();
// Collection consentTierCollection = new LinkedHashSet();
//
// consentTierCollection = cp.getConsentTierCollection();
// System.out.println("Creating CPR");
// Iterator consentTierItr = consentTierCollection.iterator();
// System.out.println("Creating CPR");
// while(consentTierItr.hasNext())
// {
// ConsentTier consent= (ConsentTier) consentTierItr.next();
// ConsentTierResponse response= new ConsentTierResponse();
// response.setResponse("Yes");
// response.setConsentTier(consent);
// consentTierResponseCollection.add(response);
// }
//
//
// collectionProtocolRegistration.setConsentTierResponseCollection(consentTierResponseCollection);
try {
collectionProtocolRegistration =
(CollectionProtocolRegistration)
appService.createObject(collectionProtocolRegistration);
} catch (Exception e) {
Logger.out.error(e.getMessage(), e);
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
BizTestCaseUtility.setNameObjectMap("CPRWithScientistAsPI", collectionProtocolRegistration);
SpecimenCollectionGroup scg = new SpecimenCollectionGroup();
scg = (SpecimenCollectionGroup) BaseTestCaseUtility.createSCG(collectionProtocolRegistration);
Site site = new Site();
site.setId(new Long(BizTestCaseUtility.CP_WITH_ALLOW_READ_PRIV));
scg.setSpecimenCollectionSite(site);
scg.setName("New SCG" + UniqueKeyGeneratorUtil.getUniqueKey());
scg = (SpecimenCollectionGroup) BaseTestCaseUtility.setEventParameters(scg);
scg.setSurgicalPathologyNumber("SPN" + UniqueKeyGeneratorUtil.getUniqueKey());
System.out.println("Creating SCG");
try {
scg = (SpecimenCollectionGroup) appService.createObject(scg);
System.out.println("SCG::" + scg.getName());
} catch (Exception e) {
Logger.out.error(e.getMessage(), e);
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
IdentifiedSurgicalPathologyReport identifiedSurgicalPathologyReport =
new IdentifiedSurgicalPathologyReport();
identifiedSurgicalPathologyReport.setActivityStatus(Status.ACTIVITY_STATUS_ACTIVE.toString());
identifiedSurgicalPathologyReport.setCollectionDateTime(new Date());
identifiedSurgicalPathologyReport.setIsFlagForReview(new Boolean(false));
identifiedSurgicalPathologyReport.setReportStatus(CaTIESConstants.PENDING_FOR_DEID);
identifiedSurgicalPathologyReport.setReportSource(site);
TextContent textContent = new TextContent();
String data =
"[FINAL DIAGNOSIS]\n"
+ "This is the Final Diagnosis Text"
+ "\n\n[GROSS DESCRIPTION]"
+ "The specimen is received unfixed labeled hernia sac and consists of a soft, pink to yellow segment of fibrous and fatty tissue measuring 7.5cm in length x 3.2 x 0.9cm with a partly defined lumen. Representative tissue submitted labeled 1A.";
textContent.setData(data);
textContent.setSurgicalPathologyReport(identifiedSurgicalPathologyReport);
Set reportSectionCollection = new HashSet();
ReportSection reportSection1 = new ReportSection();
reportSection1.setName("GDT");
reportSection1.setDocumentFragment(
"The specimen is received unfixed labeled hernia sac and consists of a soft, pink to yellow segment of fibrous and fatty tissue measuring 7.5cm in length x 3.2 x 0.9cm with a partly defined lumen. Representative tissue submitted labeled 1A.");
reportSection1.setTextContent(textContent);
ReportSection reportSection2 = new ReportSection();
reportSection2.setName("FIN");
reportSection2.setDocumentFragment("This is the Final Diagnosis Text");
reportSection2.setTextContent(textContent);
reportSectionCollection.add(reportSection1);
reportSectionCollection.add(reportSection2);
textContent.setReportSectionCollection(reportSectionCollection);
identifiedSurgicalPathologyReport.setTextContent(textContent);
identifiedSurgicalPathologyReport.setSpecimenCollectionGroup(scg);
scg.setSurgicalPathologyNumber("SPN" + UniqueKeyGeneratorUtil.getUniqueKey());
try {
identifiedSurgicalPathologyReport =
(IdentifiedSurgicalPathologyReport)
appService.createObject(identifiedSurgicalPathologyReport);
} catch (Exception e) {
Logger.out.error(e.getMessage(), e);
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
BizTestCaseUtility.setObjectMap(
identifiedSurgicalPathologyReport, IdentifiedSurgicalPathologyReport.class);
BizTestCaseUtility.setNameObjectMap("SCGWithScientistAsPI", scg);
// TissueSpecimen specimenObj = (TissueSpecimen) BaseTestCaseUtility.initTissueSpecimen();
// specimenObj.setSpecimenCollectionGroup(scg);
// StorageContainer sc = new StorageContainer();
// sc.setId(new Long(1));
// specimenObj.setStorageContainer(sc);
// specimenObj.setPositionDimensionOne(new Integer(3));
// specimenObj.setPositionDimensionTwo(new Integer(1));
// try{
// specimenObj = (TissueSpecimen) appService.createObject(specimenObj);
// System.out.println("Mol Specimen:"+ specimenObj.getLabel());
// }
// catch(Exception e){
// Logger.out.error(e.getMessage(),e);
// e.printStackTrace();
// assertFalse("Failed to register participant", true);
// }
} catch (Exception e) {
Logger.out.error(e.getMessage(), e);
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
}
/**
* Retrieves the records for class name in sourceObjectName according to field values passed in
* the passed session.
*
* @param whereColumnName An array of field names.
* @param whereColumnCondition The comparision condition for the field values.
* @param whereColumnValue An array of field values.
* @param joinCondition The join condition.
* @param The session object.
*/
public List retrieve(
String sourceObjectName,
String[] selectColumnName,
String[] whereColumnName,
String[] whereColumnCondition,
Object[] whereColumnValue,
String joinCondition)
throws DAOException {
List list = null;
try {
StringBuffer sqlBuff = new StringBuffer();
String className = Utility.parseClassName(sourceObjectName);
// Logger.out.debug("***********className:"+className);
if (selectColumnName != null && selectColumnName.length > 0) {
sqlBuff.append("Select ");
// Added by Aarti
// --------------------------------
// if(sourceObjectName.equals(Site.class.getName()))
// {
// sqlBuff.append(className + "." + Constants.SYSTEM_IDENTIFIER);
// sqlBuff.append(", ");
// }
// ---------------------------------
for (int i = 0; i < selectColumnName.length; i++) {
sqlBuff.append(className + "." + selectColumnName[i]);
if (i != selectColumnName.length - 1) {
sqlBuff.append(", ");
}
}
sqlBuff.append(" ");
}
// Logger.out.debug(" String : "+sqlBuff.toString());
Query query = null;
sqlBuff.append("from " + sourceObjectName + " " + className);
// Logger.out.debug(" String : "+sqlBuff.toString());
if ((whereColumnName != null && whereColumnName.length > 0)
&& (whereColumnCondition != null && whereColumnCondition.length == whereColumnName.length)
&& (whereColumnValue != null)) {
if (joinCondition == null) joinCondition = Constants.AND_JOIN_CONDITION;
sqlBuff.append(" where ");
// Adds the column name and search condition in where clause.
for (int i = 0; i < whereColumnName.length; i++) {
sqlBuff.append(className + "." + whereColumnName[i] + " ");
if (whereColumnCondition[i].indexOf("in") != -1) {
sqlBuff.append(whereColumnCondition[i] + "( ");
Object valArr[] = (Object[]) whereColumnValue[i];
for (int j = 0; j < valArr.length; j++) {
// Logger.out.debug(sqlBuff);
sqlBuff.append("? ");
if ((j + 1) < valArr.length) sqlBuff.append(", ");
}
sqlBuff.append(") ");
} else if (whereColumnCondition[i].indexOf("is not null") != -1) {
sqlBuff.append(whereColumnCondition[i]);
} else if (whereColumnCondition[i].indexOf("is null") != -1) {
sqlBuff.append(whereColumnCondition[i]);
} else {
sqlBuff.append(whereColumnCondition[i] + " ? ");
}
if (i < (whereColumnName.length - 1)) sqlBuff.append(" " + joinCondition + " ");
}
// Logger.out.debug(sqlBuff.toString());
query = session.createQuery(sqlBuff.toString());
int index = 0;
// Adds the column values in where clause
for (int i = 0; i < whereColumnValue.length; i++) {
// Logger.out.debug("whereColumnValue[i]. " + whereColumnValue[i]);
if (whereColumnCondition[i].equals("is null")
|| whereColumnCondition[i].equals("is not null")) {
} else {
Object obj = whereColumnValue[i];
if (obj instanceof Object[]) {
Object[] valArr = (Object[]) obj;
for (int j = 0; j < valArr.length; j++) {
query.setParameter(index, valArr[j]);
index++;
}
} else {
query.setParameter(index, obj);
index++;
}
}
}
} else {
query = session.createQuery(sqlBuff.toString());
}
list = query.list();
// Added by Aarti
// --------------------------------
// if(sourceObjectName.equals(Site.class.getName()))
// {
// boolean isAuthorized;
// Object[] objects = null;
// Object[] newObjects = null;
// Long id;
// Site site;
//
// if (selectColumnName != null && selectColumnName.length > 0)
// {
// if(list != null)
// {
// for(int i=0; i<list.size();)
// {
// objects = (Object[]) list.get(i);
//
// if(objects != null)
// {
// newObjects = new Object[objects.length-1];
// id = (Long) objects[0];
// isAuthorized = SecurityManager.getInstance(this.getClass())
// .isAuthorized("*****@*****.**",
// sourceObjectName+"_"+id,
// Permissions.USE);
// Logger.out.debug(" User's Authorization to update
// "+sourceObjectName+"_"+id+" "+isAuthorized);
// list.remove(i);
// if(isAuthorized)
// {
// for(int x = 1;x<objects.length;x++ )
// {
// newObjects[x-1] = objects[x];
// }
// list.add(i,newObjects);
// i++;
// }
// }
// }
// }
// }
// else
// {
// if(list != null)
// {
// for(int i=0; i<list.size();)
// {
// site = (Site) list.get(i);
// if(site !=null)
// {
// isAuthorized = SecurityManager.getInstance(this.getClass())
// .isAuthorized("*****@*****.**",
// sourceObjectName+"_"+site.getId(),
// Permissions.USE);
// Logger.out.debug(" User's Authorization to update
// "+sourceObjectName+"_"+site.getId()+" "+isAuthorized);
//
// if(isAuthorized)
// {
// i++;
// }
// else
// {
// list.remove(i);
// }
// }
// }
// }
// }
// }
// ---------------------------------
// Logger.out.debug(" String : " + sqlBuff.toString());
} catch (HibernateException hibExp) {
Logger.out.error(hibExp.getMessage(), hibExp);
throw new DAOException("Error in retrieve " + hibExp.getMessage(), hibExp);
} catch (Exception exp) {
Logger.out.error(exp.getMessage(), exp);
throw new DAOException("Logical Erroe in retrieve method " + exp.getMessage(), exp);
}
return list;
}