public String updateDomain(Domain theDomain) throws Exception {
try {
startTransaction(false);
DomainRow dr = new DomainRow();
dr.id = idAsInt(theDomain.getId());
dr.name = theDomain.getName();
dr.description = theDomain.getDescription();
dr.className = theDomain.getDriverClassName();
dr.propFileName = theDomain.getPropFileName();
dr.authenticationServer = theDomain.getAuthenticationServer();
dr.theTimeStamp = theDomain.getTheTimeStamp();
dr.silverpeasServerURL = theDomain.getSilverpeasServerURL();
// Create domain
getOrganization().domain.updateDomain(dr);
if (domainDriverInstances.get(theDomain.getId()) != null) {
domainDriverInstances.remove(theDomain.getId());
}
this.commit();
LoginPasswordAuthentication.initDomains();
return theDomain.getId();
} catch (AdminException e) {
try {
this.rollback();
} catch (Exception e1) {
SilverTrace.error("admin", "DomainDriverManager.updateDomain", "root.EX_ERR_ROLLBACK", e1);
}
throw new AdminException(
"DomainDriverManager.updateDomain",
SilverpeasException.ERROR,
"admin.EX_ERR_ADD_DOMAIN",
"domain name: '" + theDomain.getName() + "'",
e);
} finally {
releaseOrganizationSchema();
}
}
private void loadGroup(DomainFile domainFile, String gene, DomainAcc acc, Polypeptide polypeptide)
throws IOException {
logger.debug("In loadGroup()");
DbXRef interProDbxref = null;
if (acc != DomainAcc.NULL && analysis.getProgram().equals("iprscan")) {
logger.debug(
String.format(
"Creating InterPro dbxref for '%s' with description '%s'",
acc.getId(), acc.getDescription()));
interProDbxref = objectManager.getDbXRef("InterPro", acc.getId(), acc.getDescription());
}
int n = -1;
for (DomainRow row : domainFile.rows(gene, acc)) {
n++;
logger.debug(row);
// Insert polypeptide_domain
DbXRef dbxref = objectManager.getDbXRef(row.db(), row.nativeAcc(), row.nativeDesc());
if (dbxref == null) {
throw new RuntimeException(
String.format("Could not find database '%s' on line %d", row.db(), row.lineNumber()));
}
String domainUniqueName;
String accessionNumber = acc.getId();
if (accessionNumber == null) {
accessionNumber = row.nativeAcc();
}
if (n == 0) {
domainUniqueName =
String.format("%s:%s:%s", polypeptide.getUniqueName(), row.db(), accessionNumber);
} else {
domainUniqueName =
String.format("%s:%s:%s:%d", polypeptide.getUniqueName(), row.db(), accessionNumber, n);
}
PolypeptideDomain polypeptideDomain =
sequenceDao.createPolypeptideDomain(
domainUniqueName,
polypeptide,
row.score(),
row.acc().getDescription(),
row.fmin(),
row.fmax(),
dbxref,
row.evalue(),
analysis);
// add GO terms
addGoTerms(row.getGoTerms(), polypeptide, polypeptideDomain, row.getGoTermComment());
// link to InterPro dbxref if applicable
if (interProDbxref != null && analysis.getProgram().equals("iprscan")) {
FeatureDbXRef featureDbXRef = new FeatureDbXRef(interProDbxref, polypeptideDomain, true);
sequenceDao.persist(featureDbXRef);
polypeptideDomain.addFeatureDbXRef(featureDbXRef);
}
}
}
