public Entity updateEntity(Entity entity) throws ApplicationException {
if (entity == null) {
return entity;
}
if (entity.getEntityVersionId() == null) {
throw new ApplicationException(
"An entity definition must first be created before it is updated.");
}
try {
Date currentDate = new Date();
entity.setDateChanged(currentDate);
entity.setUserChangedBy(Context.getUserContext().getUser());
for (EntityAttribute attrib : entity.getAttributes()) {
if (attrib.getDateCreated() == null) {
attrib.setDateCreated(currentDate);
attrib.setUserCreatedBy(Context.getUserContext().getUser());
// attrib.setEntity(entity);
}
attrib.setEntity(entity);
}
// Mark deletion attributes
handleAttributeUpdates(entity);
// remove validations for marked attribute
for (EntityAttribute attrib : entity.getAttributes()) {
if (attrib.getUserVoidedBy() != null) {
// remove validations
List<EntityAttributeValidation> existingValidations =
loadEntityAttributeValidations(attrib);
for (EntityAttributeValidation validation : existingValidations) {
deleteEntityAttributeValidation(validation);
}
}
}
Entity updatedEntity = entityDefinitionDao.updateEntity(entity);
updatedEntity = entityDefinitionDao.loadEntity(entity.getEntityVersionId());
addToCache(updatedEntity);
Context.notifyObserver(ObservationEventType.ENTITY_ATTRIBUTE_UPDATE_EVENT, entity);
return updatedEntity;
} catch (DaoException e) {
throw new ApplicationException(e.getMessage());
}
}
public void deleteCustomField(CustomField field) throws ApplicationException {
if (field == null
|| ConvertUtil.isNullOrEmpty(field.getEntityName())
|| ConvertUtil.isNullOrEmpty(field.getFieldName())) {
log.warn("The custom field to be deleted is invalid: " + field);
throw new ApplicationException("Unable to add invalid custom field definition.");
}
Entity entity = findLatestEntityVersionByName(field.getEntityName());
EntityAttribute attrib = null;
for (EntityAttribute item : entity.getAttributes()) {
if (item.getName().equalsIgnoreCase(field.getFieldName()) && item.getDateVoided() == null) {
attrib = item;
}
}
if (attrib == null) {
log.info("The user attempted to delete a custom field that does not exist.");
throw new ApplicationException("Unable to delete an unknown custom field definition.");
}
attrib.setDateVoided(new Date());
attrib.setUserVoidedBy(Context.getUserContext().getUser());
try {
entityDefinitionDao.updateEntity(entity);
// Generate a notification event to inform interested listeners via the lightweight mechanism
// that this event has occurred.
Context.notifyObserver(ObservationEventType.CUSTOM_FIELD_DELETE_EVENT, field);
} catch (DaoException e) {
log.error("Failed while deleting a custom field: " + e, e);
throw new ApplicationException("Failed while deleting the custom field: " + e.getMessage());
}
}
public List<Entity> findEntitiesByName(String name) {
List<Entity> entities = entityDefinitionDao.findEntitiesByName(name);
for (Entity entity : entities) {
addToCache(entity);
}
return entities;
}
public Entity addEntity(Entity entity) throws ApplicationException {
if (entity == null) {
return null;
}
if (entity.getEntityVersionId() != null) {
throw new ApplicationException(
"This entity definition already exists so it can only be updated.");
}
validateNameUniqueness(entity);
try {
entity.setUserCreatedBy(Context.getUserContext().getUser());
Date dateCreated = new Date();
entity.setDateCreated(dateCreated);
for (EntityAttribute attribute : entity.getAttributes()) {
attribute.setDateCreated(dateCreated);
attribute.setUserCreatedBy(Context.getUserContext().getUser());
attribute.setEntity(entity);
}
entityDefinitionDao.addEntity(entity);
addToCache(entity);
Context.notifyObserver(ObservationEventType.ENTITY_ADD_EVENT, entity);
return entity;
} catch (DaoException e) {
throw new ApplicationException(e.getMessage());
}
}
public void updateEntityAttributeGroups(List<EntityAttributeGroup> groups, Entity updatedEntity)
throws ApplicationException {
if (groups == null) {
return;
}
Entity existing = entityDefinitionDao.loadEntity(updatedEntity.getEntityVersionId());
List<EntityAttributeGroup> existingGroups = loadEntityAttributeGroups(existing);
Map<Integer, EntityAttributeGroup> newGroupById = new HashMap<Integer, EntityAttributeGroup>();
for (EntityAttributeGroup group : groups) {
newGroupById.put(group.getEntityAttributeGroupId(), group);
}
// remove deleted groups
for (EntityAttributeGroup group : existingGroups) {
if (newGroupById.get(group.getEntityAttributeGroupId()) == null) {
deleteEntityAttributeGroup(group);
}
}
for (EntityAttributeGroup newgroup : groups) {
if (newgroup.getEntityAttributeGroupId() != null) {
updateEntityAttributeGroup(newgroup);
} else {
addEntityAttributeGroup(newgroup);
}
}
}
public void updateEntityAttributeValidations(
List<EntityAttributeValidation> validations, Entity updatedEntity, String attributeName)
throws ApplicationException {
if (validations == null) {
return;
}
Entity existing = entityDefinitionDao.loadEntity(updatedEntity.getEntityVersionId());
EntityAttribute existingAttribute = existing.findAttributeByName(attributeName);
List<EntityAttributeValidation> existingValidations =
loadEntityAttributeValidations(existingAttribute);
Map<Integer, EntityAttributeValidation> newValidationById =
new HashMap<Integer, EntityAttributeValidation>();
for (EntityAttributeValidation validation : validations) {
if (validation.getEntityAttributeValidationId() != null) {
newValidationById.put(validation.getEntityAttributeValidationId(), validation);
}
}
// remove deleted validations
for (EntityAttributeValidation validation : existingValidations) {
if (newValidationById.get(validation.getEntityAttributeValidationId()) == null) {
deleteEntityAttributeValidation(validation);
}
}
for (EntityAttributeValidation newValidation : validations) {
if (newValidation.getEntityAttributeValidationId() != null) {
updateEntityAttributeValidation(newValidation);
} else {
addEntityAttributeValidation(newValidation);
}
}
}
public List<Entity> loadEntities() {
List<Entity> entities = entityDefinitionDao.loadEntities();
// Since we got all of them again, we might as well update the cache
for (Entity entity : entities) {
addToCache(entity);
}
return entities;
}
public Entity loadEntity(Integer id) {
Entity entity = getFromCache(id);
if (entity != null) {
return entity;
}
entity = entityDefinitionDao.loadEntity(id);
return entity;
}
public void dropEntityIndexes(Integer entityVersionId) throws ApplicationException {
if (entityVersionId == null) {
return;
}
Entity entity = entityDefinitionDao.loadEntity(entityVersionId);
if (entity == null) {
log.info("A request was made to drop the indexes for an unknown entity.");
return;
}
entityDao.dropIndexes(entity);
}
public CustomField findCustomField(String entityName, String fieldName) {
Entity entity = findLatestEntityVersionByName(entityName);
if (entity == null) {
return null;
}
EntityAttribute attrib = entityDefinitionDao.findCustomField(entity, fieldName);
if (attrib == null) {
return null;
}
CustomField field = buildCustomFieldFromAttribute(attrib);
if (log.isDebugEnabled()) {
log.debug("Found custom field: " + field);
}
return field;
}
public void deleteEntityAttributeValidation(EntityAttributeValidation validation)
throws ApplicationException {
if (validation == null) {
return;
}
if (validation.getEntityAttributeValidationId() == null) {
throw new ApplicationException(
"An entity attribute validation must first be created before it is deleted.");
}
try {
entityDefinitionDao.deleteEntityAttributeValidation(validation);
} catch (DaoException e) {
throw new ApplicationException(e.getMessage());
}
}
public void deleteEntityAttributeGroup(EntityAttributeGroup entityAttributeGroup)
throws ApplicationException {
if (entityAttributeGroup == null) {
return;
}
if (entityAttributeGroup.getEntityAttributeGroupId() == null) {
throw new ApplicationException(
"An entity attribute group must first be created before it is deleted.");
}
try {
entityDefinitionDao.deleteEntityAttributeGroup(entityAttributeGroup);
} catch (DaoException e) {
throw new ApplicationException(e.getMessage());
}
}
/** Will export the entity passed in as the entity version id into a string. */
public String exportEntity(Integer entityVersionId) throws ApplicationException {
if (entityVersionId == null) {
return "";
}
Entity entity = entityDefinitionDao.loadEntity(entityVersionId);
try {
// 1. convert Entity to EntityModel
EntityModel entityModel = ConvertUtil.mapToEntityModel(entity, EntityModel.class);
// 2. set group info to EntityModel
List<EntityAttributeGroup> groups = loadEntityAttributeGroups(entity);
entityModel = ConvertUtil.setGroupInfoToEntityModel(groups, entityModel);
// 3. set validation info to entity attribute
for (EntityAttribute attribute : entity.getAttributes()) {
List<EntityAttributeValidation> validations = loadEntityAttributeValidations(attribute);
ValidationsType validationsType = ConvertUtil.mapToEntityValidations(validations);
// set validations info to attributeType
AttributesType attributesType = entityModel.getAttributes();
if (attributesType != null) {
for (AttributeType attributeType : attributesType.getAttribute()) {
String name = attributeType.getName();
if (attribute.getName().equals(name)) {
attributeType.setValidations(validationsType);
}
}
}
}
// export to xml format
JAXBContext jaxbContext = JAXBContext.newInstance(EntityModel.class);
Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
OutputStream outputStream = new ByteArrayOutputStream();
jaxbMarshaller.marshal(entityModel, outputStream);
return outputStream.toString();
} catch (JAXBException e) {
log.warn("Unable to serialize a Entity into a string: " + e, e);
throw new RuntimeException(e);
}
}
public List<CustomField> loadCustomFields(String entityName) {
Entity entity = findLatestEntityVersionByName(entityName);
if (entity == null) {
return new ArrayList<CustomField>();
}
List<EntityAttribute> attribs = entityDefinitionDao.loadCustomFields(entity);
List<CustomField> fields = new ArrayList<CustomField>(attribs.size());
if (attribs.size() == 0) {
return fields;
}
for (EntityAttribute attrib : attribs) {
CustomField field = buildCustomFieldFromAttribute(attrib);
fields.add(field);
}
return fields;
}
private void handleAttributeUpdates(Entity entity) {
Entity existing = entityDefinitionDao.loadEntity(entity.getEntityVersionId());
Map<Integer, EntityAttribute> newAttribById = new HashMap<Integer, EntityAttribute>();
for (EntityAttribute attribute : entity.getAttributes()) {
newAttribById.put(attribute.getEntityAttributeId(), attribute);
}
// Mark for deletion attributes that were removed
for (EntityAttribute attrib : existing.getAttributes()) {
if (newAttribById.get(attrib.getEntityAttributeId()) == null) {
attrib.setDateVoided(entity.getDateChanged());
attrib.setUserVoidedBy(Context.getUserContext().getUser());
entity.addAttribute(attrib);
}
}
}
public EntityAttributeValidation addEntityAttributeValidation(
EntityAttributeValidation validation) throws ApplicationException {
if (validation == null
|| validation.getEntityAttribute() == null
|| validation.getParameters() == null) {
throw new ApplicationException("This entity attribute validation is invalid.");
}
if (validation.getEntityAttributeValidationId() != null) {
throw new ApplicationException(
"This entity attribute validation already exists so it can only be updated.");
}
try {
entityDefinitionDao.addEntityAttributeValidation(validation);
return validation;
} catch (DaoException e) {
throw new ApplicationException(e.getMessage());
}
}
public EntityAttributeGroup addEntityAttributeGroup(EntityAttributeGroup entityAttributeGroup)
throws ApplicationException {
if (entityAttributeGroup == null
|| entityAttributeGroup.getEntity() == null
|| entityAttributeGroup.getEntityAttributes() == null) {
throw new ApplicationException("This entity attribute group is invalid.");
}
if (entityAttributeGroup.getEntityAttributeGroupId() != null) {
throw new ApplicationException(
"This entity attribute group already exists so it can only be updated.");
}
try {
entityDefinitionDao.addEntityAttributeGroup(entityAttributeGroup);
return entityAttributeGroup;
} catch (DaoException e) {
throw new ApplicationException(e.getMessage());
}
}
public CustomField addCustomField(CustomField field) throws ApplicationException {
if (field == null
|| ConvertUtil.isNullOrEmpty(field.getEntityName())
|| ConvertUtil.isNullOrEmpty(field.getFieldName())
|| ConvertUtil.isNullOrEmpty(field.getSourceFieldName())) {
log.info("The custom field to be added is invalid: " + field);
throw new ApplicationException("Unable to add invalid custom field definition.");
}
// Validate that a custom field by the same name does not already exist.
List<CustomField> fields = loadCustomFields(field.getEntityName());
for (CustomField custom : fields) {
if (custom.getFieldName().equalsIgnoreCase(field.getFieldName())) {
log.warn(
"User attempted to add a custom field "
+ field
+ " that already exists in the system.");
throw new ApplicationException(
"Unable to add a custom field that already exists in the system.");
}
}
Entity entity = findLatestEntityVersionByName(field.getEntityName());
try {
EntityAttribute attribute = buildAttributeFromCustomField(entity, field);
entity.addAttribute(attribute);
// TODO: Validate that the source field is known
// TODO: Validate that the transformation function is known
attribute = entityDefinitionDao.addCustomField(entity, attribute);
// Generate a notification event to inform interested listeners via the lightweight mechanism
// that this event has occurred.
Context.notifyObserver(ObservationEventType.CUSTOM_FIELD_ADD_EVENT, field);
Context.notifyObserver(ObservationEventType.ENTITY_ATTRIBUTE_UPDATE_EVENT, entity);
return field;
} catch (DaoException e) {
log.error("Failed while saving a custom field: " + e, e);
throw new ApplicationException("Failed while saving the custom field: " + e.getMessage());
}
}
public void deleteEntity(Entity entity) throws ApplicationException {
if (entity == null) {
return;
}
if (entity.getEntityVersionId() == null) {
throw new ApplicationException(
"An entity definition must first be created before it is deleted.");
}
try {
Date dateVoided = new Date();
entity.setDateVoided(dateVoided);
entity.setUserVoidedBy(Context.getUserContext().getUser());
for (EntityAttribute attribute : entity.getAttributes()) {
attribute.setDateVoided(dateVoided);
attribute.setUserVoidedBy(Context.getUserContext().getUser());
attribute.setEntity(entity);
}
entityDefinitionDao.updateEntity(entity);
addToCache(entity);
} catch (DaoException e) {
throw new ApplicationException(e.getMessage());
}
}
/** Will import the entity definition specified in the relative filename of the parameter. */
public void importEntity(String filename) throws ApplicationException {
if (filename.isEmpty()) {
return;
}
try {
File file = new File(filename);
log.debug("Loading file " + file.getAbsolutePath());
if (!file.isFile() || !file.canRead()) {
log.error("Input file is not available.");
throw new RuntimeException("Input file " + filename + " is not readable.");
}
// Import from file
JAXBContext jaxbContext = JAXBContext.newInstance(EntityModel.class);
Unmarshaller unJaxbMarshaller = jaxbContext.createUnmarshaller();
EntityModel entityModel = (EntityModel) unJaxbMarshaller.unmarshal(new FileInputStream(file));
// convert EntityModel to Entity, EntityAttributeGroups, EntityAttributeValidations
Entity entity =
ConvertUtil.mapToEntityModel(entityModel, getEntityAttributeDatatypes(), Entity.class);
// check existing entity
List<Entity> entities = entityDefinitionDao.findEntitiesByName(entity.getName());
for (Entity en : entities) {
if (en.getVersionId().intValue() == entity.getVersionId().intValue()) {
log.error("Entity definition already exists: " + entity.getName());
throw new RuntimeException(
"Entity definition in the file " + filename + " already exists.");
}
}
// add entity
Entity newEntity = addEntity(entity);
// 2. add entity groups with attribute
List<EntityAttributeGroup> groups =
ConvertUtil.mapToEntityGroup(
entityModel, newEntity, org.openhie.openempi.model.EntityAttributeGroup.class);
for (EntityAttributeGroup group : groups) {
addEntityAttributeGroup(group);
}
// 3. add entity attribute validations
for (AttributeType attributeType : entityModel.getAttributes().getAttribute()) {
List<EntityAttributeValidation> validations =
ConvertUtil.mapToEntityValidations(
attributeType,
newEntity,
org.openhie.openempi.model.EntityAttributeValidation.class);
for (EntityAttributeValidation validation : validations) {
addEntityAttributeValidation(validation);
}
}
return;
} catch (Exception e) {
log.warn("Unable to Unmarshal xml to a EntityModel: " + e, e);
throw new RuntimeException(e);
}
}
public List<EntityAttributeDatatype> getEntityAttributeDatatypes() {
if (datatypes == null) {
datatypes = entityDefinitionDao.getEntityAttributeDatatypes();
}
return datatypes;
}
public EntityAttributeGroup loadEntityAttributeGroup(Integer id) {
return entityDefinitionDao.loadEntityAttributeGroup(id);
}
public List<EntityAttributeGroup> loadEntityAttributeGroups(Entity entity) {
return entityDefinitionDao.loadEntityAttributeGroups(entity);
}
public EntityAttributeValidation loadEntityAttributeValidation(Integer id) {
return entityDefinitionDao.loadEntityAttributeValidation(id);
}
public List<EntityAttributeValidation> loadEntityAttributeValidations(
EntityAttribute entityAttribute) {
return entityDefinitionDao.loadEntityAttributeValidations(entityAttribute);
}