uk.ac.ebi.intact.core.persistence.dao.BioSourceDao java code examples

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/**
 * Prints the most counts in the database.
 * @param ps The printStream to use
 *
 * @since 1.9.0
 */
public static void printDatabaseCounts(PrintStream ps) {
  final DaoFactory daoFactory = IntactContext.getCurrentInstance().getDataContext().getDaoFactory();
  ps.println("Publications: "+ daoFactory.getPublicationDao().countAll());
  ps.println("\tXrefs: "+ daoFactory.getXrefDao(PublicationXref.class).countAll());
  ps.println("\tAliases: "+ daoFactory.getAliasDao(PublicationAlias.class).countAll());
  ps.println("Experiments: "+ daoFactory.getExperimentDao().countAll());
  ps.println("\tXrefs: "+ daoFactory.getXrefDao(ExperimentXref.class).countAll());
  ps.println("\tAliases: "+ daoFactory.getAliasDao(ExperimentAlias.class).countAll());
  ps.println("Interactors: "+ daoFactory.getInteractorDao().countAll());
  ps.println("\tInteractions: "+ daoFactory.getInteractionDao().countAll());
  ps.println("\tPolymers: " + daoFactory.getPolymerDao().countAll());
  ps.println("\t\tProteins: "+ daoFactory.getProteinDao().countAll());
  ps.println("\t\tNucleic Acids: "+ daoFactory.getInteractorDao(NucleicAcidImpl.class).countAll());
  ps.println("\tSmall molecules: " + daoFactory.getInteractorDao(SmallMoleculeImpl.class).countAll());
  ps.println("\tInteractor Xrefs: "+ daoFactory.getXrefDao(InteractorXref.class).countAll());
  ps.println("\tInteractor Aliases: "+ daoFactory.getAliasDao(InteractorAlias.class).countAll());
  ps.println("Components: "+ daoFactory.getComponentDao().countAll());
  ps.println("Features: "+ daoFactory.getFeatureDao().countAll());
  ps.println("\tRanges: "+ daoFactory.getRangeDao().countAll());
  ps.println("CvObjects: "+ daoFactory.getCvObjectDao().countAll());
  ps.println("BioSources: "+ daoFactory.getBioSourceDao().countAll());
  ps.println("Annotations: "+ daoFactory.getAnnotationDao().countAll());
  ps.println("Institutions: "+ daoFactory.getInstitutionDao().countAll());
}

/**
 * Search the IntAct database and retreive a BioSource having the given taxid and no CvCellType or CvTissue.
 *
 * @param taxid a non null taxid.
 * @return a BioSource or null if none is found.
 */
private BioSource searchIntactByTaxid(String taxid) throws BioSourceServiceException {
  log.debug("Searching in the database for BioSource(" + taxid + ")");
  DataContext dataContext = IntactContext.getCurrentInstance().getDataContext();
  TransactionStatus transactionStatus = dataContext.beginTransaction();
  BioSourceDao bsDao = dataContext.getDaoFactory().getBioSourceDao();
  BioSource biosource = bsDao.getByTaxonIdUnique(taxid);
  try {
    dataContext.commitTransaction(transactionStatus);
  } catch (IntactTransactionException e) {
    throw new BioSourceServiceException("Problem committing", e);
  }
  if (log.isDebugEnabled()) {
    if (biosource == null) {
      log.debug("Could not find Biosource having taxid: " + taxid);
    } else {
      log.debug("Found 1 biosource: " + biosource.getShortLabel() + " [" + biosource.getAc() + "]");
    }
  }
  return biosource;
}

sourceDao.saveOrUpdate(bioSource);

final List<BioSource> bioSources = daoFactory.getBioSourceDao().getAll();

/**
 * Prints the most counts in the database.
 * @param ps The printStream to use
 *
 * @since 1.9.0
 */
public static void printDatabaseCounts(PrintStream ps) {
  final DaoFactory daoFactory = IntactContext.getCurrentInstance().getDataContext().getDaoFactory();
  ps.println("Publications: "+ daoFactory.getPublicationDao().countAll());
  ps.println("\tXrefs: "+ daoFactory.getXrefDao(PublicationXref.class).countAll());
  ps.println("\tAliases: "+ daoFactory.getAliasDao(PublicationAlias.class).countAll());
  ps.println("Experiments: "+ daoFactory.getExperimentDao().countAll());
  ps.println("\tXrefs: "+ daoFactory.getXrefDao(ExperimentXref.class).countAll());
  ps.println("\tAliases: "+ daoFactory.getAliasDao(ExperimentAlias.class).countAll());
  ps.println("Interactors: "+ daoFactory.getInteractorDao().countAll());
  ps.println("\tInteractions: "+ daoFactory.getInteractionDao().countAll());
  ps.println("\tPolymers: " + daoFactory.getPolymerDao().countAll());
  ps.println("\t\tProteins: "+ daoFactory.getProteinDao().countAll());
  ps.println("\t\tNucleic Acids: "+ daoFactory.getInteractorDao(NucleicAcidImpl.class).countAll());
  ps.println("\tSmall molecules: " + daoFactory.getInteractorDao(SmallMoleculeImpl.class).countAll());
  ps.println("\tInteractor Xrefs: "+ daoFactory.getXrefDao(InteractorXref.class).countAll());
  ps.println("\tInteractor Aliases: "+ daoFactory.getAliasDao(InteractorAlias.class).countAll());
  ps.println("Components: "+ daoFactory.getComponentDao().countAll());
  ps.println("Features: "+ daoFactory.getFeatureDao().countAll());
  ps.println("\tRanges: "+ daoFactory.getRangeDao().countAll());
  ps.println("CvObjects: "+ daoFactory.getCvObjectDao().countAll());
  ps.println("BioSources: "+ daoFactory.getBioSourceDao().countAll());
  ps.println("Annotations: "+ daoFactory.getAnnotationDao().countAll());
  ps.println("Institutions: "+ daoFactory.getInstitutionDao().countAll());
}

Javadoc

To access to biosources

Most used methods

countAll
getAll
getByTaxonIdUnique
Searches for a BioSource having the given taxid and no CvTissue or CvCellType.
saveOrUpdate

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How to useBioSourceDao in uk.ac.ebi.intact.core.persistence.dao

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