private void parseAccessionNumber(Accessions accession, IdentifierType value) {
String composite = value.getComposite();
if (composite != null) {
StringTokenizer st = new StringTokenizer(composite, "./-");
int count = 0;
String thisToken;
while (st.hasMoreTokens()) {
count++;
thisToken = StringHelper.cleanUpWhiteSpace((String) st.nextElement());
if (count == 1) {
accession.setAccessionNumber1(
StringHelper.trimToLength(
thisToken,
ATFieldInfo.checkFieldLength(
Accessions.class, Accessions.PROPERTYNAME_ACCESSION_NUMBER_1)));
} else if (count == 2) {
accession.setAccessionNumber2(
StringHelper.trimToLength(
thisToken,
ATFieldInfo.checkFieldLength(
Accessions.class, Accessions.PROPERTYNAME_ACCESSION_NUMBER_2)));
} else if (count == 3) {
accession.setAccessionNumber3(
StringHelper.trimToLength(
thisToken,
ATFieldInfo.checkFieldLength(
Accessions.class, Accessions.PROPERTYNAME_ACCESSION_NUMBER_3)));
} else if (count == 4) {
accession.setAccessionNumber4(
StringHelper.trimToLength(
thisToken,
ATFieldInfo.checkFieldLength(
Accessions.class, Accessions.PROPERTYNAME_ACCESSION_NUMBER_4)));
}
}
} else {
accession.setAccessionNumber1(
cleanAndTrim(
value.getPart1(), Accessions.class, Accessions.PROPERTYNAME_ACCESSION_NUMBER_1));
if (value.getPart2() != null) {
accession.setAccessionNumber2(
cleanAndTrim(
value.getPart2(), Accessions.class, Accessions.PROPERTYNAME_ACCESSION_NUMBER_2));
}
if (value.getPart3() != null) {
accession.setAccessionNumber3(
cleanAndTrim(
value.getPart3(), Accessions.class, Accessions.PROPERTYNAME_ACCESSION_NUMBER_3));
}
if (value.getPart4() != null) {
accession.setAccessionNumber4(
cleanAndTrim(
value.getPart4(), Accessions.class, Accessions.PROPERTYNAME_ACCESSION_NUMBER_4));
}
}
}
private String cleanAndTrim(String valueToClean, Class clazz, String propertyName) {
String returnString = StringHelper.cleanUpWhiteSpace(valueToClean);
ATFieldInfo fieldInfo = ATFieldInfo.getFieldInfo(clazz, propertyName);
if (fieldInfo.getStringLengthLimit() != null && fieldInfo.getStringLengthLimit() > 0) {
return StringHelper.trimToLength(returnString, fieldInfo.getStringLengthLimit());
} else {
return returnString;
}
}
private void addResource(
Accessions accession,
IdentifierType resourceId,
DomainImportController controller,
String accesionNumber,
int recordNumber)
throws ImportException {
if (resourceId != null) {
String resourceId1;
String resourceId2 = null;
String resourceId3 = null;
String resourceId4 = null;
if (resourceId.getComposite() != null) {
resourceId1 =
StringHelper.trimToLength(
resourceId.getComposite(),
ATFieldInfo.checkFieldLength(
Resources.class, Resources.PROPERTYNAME_RESOURCE_IDENTIFIER_1));
} else {
resourceId1 = resourceId.getPart1();
resourceId2 = resourceId.getPart2();
resourceId3 = resourceId.getPart3();
resourceId4 = resourceId.getPart4();
}
ResourcesDAO resourceDao = new ResourcesDAO();
Resources resource;
if (resourceCreation.equalsIgnoreCase(AccessionImportXmlHandler.RESOURCE_CREATION_NONE)) {
resource =
resourceDao.lookupResource(
resourceId1, resourceId2, resourceId3, resourceId4, false, repository);
} else {
resource =
resourceDao.lookupResource(
resourceId1, resourceId2, resourceId3, resourceId4, true, repository);
}
if (resourceDao.getNewRecordCreated()
&& resourceCreation.equalsIgnoreCase(AccessionImportXmlHandler.RESOURCE_CREATION_FULL)) {
try {
resource = (Resources) resourceDao.findByPrimaryKeyLongSession(resource.getIdentifier());
resource.populateResourceFromAccession(accession);
resourceDao.updateLongSession(resource);
} catch (LookupException e) {
throw new ImportException(
"Error creating resource: " + resourceId + ", " + e.getMessage(), e);
} catch (PersistenceException e) {
throw new ImportException(
"Error creating resource: " + resourceId + ", " + e.getMessage(), e);
} catch (DuplicateLinkException e) {
throw new ImportException(
"Error creating resource: duplicate link" + resourceId + ", " + e.getMessage(), e);
}
}
if (resource != null) {
AccessionsResources accessionResource = new AccessionsResources(resource, accession);
accession.addAccessionsResources(accessionResource);
}
} else {
if (!resourceCreation.equalsIgnoreCase(AccessionImportXmlHandler.RESOURCE_CREATION_NONE)) {
controller.addLineToImportLog(
"Record # "
+ recordNumber
+ " - "
+ accesionNumber
+ " has no resource id so no resource record was created");
}
}
}