public <T extends Alias> AliasDao<T> getAliasDao( Class<T> aliasType ) { AliasDao aliasDao = (AliasDao) applicationContext.getBean("aliasDaoImpl"); aliasDao.setEntityClass(aliasType); return aliasDao; }
private Alias synchronizeAlias( Alias alias, AnnotatedObject parent ) { if (alias.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getAliasDao().getByAc(alias.getAc()); } alias.setCvAliasType( synchronize( alias.getCvAliasType() ) ); alias.setParent(parent); if (alias.getAc() == null && parent.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForAlias(alias), alias); } return alias; }
/** * Retrieves the aliases from an AnnotatedObject, initializing them if necessary. * * @param ao The annotated object instance with possibly non-initialized aliases * @return The returned aliases are ensured to be initialized * @since 2.4.0 */ public static Collection<? extends Alias> ensureInitializedAliases(AnnotatedObject<?, ?> ao) { Collection<? extends Alias> aliases; if (IntactCore.isInitialized(ao.getAliases())) { aliases = ao.getAliases(); } else { aliases = IntactContext.getCurrentInstance().getDaoFactory().getAliasDao(AnnotatedObjectUtils.getAliasClassType(ao.getClass())) .getByParentAc(ao.getAc()); } return aliases; }
/** * 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()); }
private Alias synchronizeAlias( Alias alias, AnnotatedObject parent ) { if (alias.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getAliasDao().getByAc(alias.getAc()); } alias.setCvAliasType( synchronize( alias.getCvAliasType() ) ); alias.setParent(parent); if (alias.getAc() == null && parent.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForAlias(alias), alias); } return alias; }
/** * Retrieves the aliases from an AnnotatedObject, initializing them if necessary. * * @param ao The annotated object instance with possibly non-initialized aliases * @return The returned aliases are ensured to be initialized * @since 2.4.0 */ public static Collection<? extends Alias> ensureInitializedAliases(AnnotatedObject<?, ?> ao) { Collection<? extends Alias> aliases; if (IntactCore.isInitialized(ao.getAliases())) { aliases = ao.getAliases(); } else { aliases = IntactContext.getCurrentInstance().getDaoFactory().getAliasDao(AnnotatedObjectUtils.getAliasClassType(ao.getClass())) .getByParentAc(ao.getAc()); } return aliases; }
/** * 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()); }
public <T extends Alias> AliasDao<T> getAliasDao( Class<T> aliasType ) { AliasDao aliasDao = (AliasDao) applicationContext.getBean("aliasDaoImpl"); aliasDao.setEntityClass(aliasType); return aliasDao; }