protected DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); } }
/** * Initializes a standalone {@code IntactContext} using a memory database. */ public static void initStandaloneContextInMemory() { initStandaloneContextInMemory((ApplicationContext) null); }
public static DaoFactory getCurrentInstance( IntactContext context ) { return context.getDataContext().getDaoFactory(); }
public DefaultFinder() { config = IntactContext.getCurrentInstance().getConfig(); }
public CoreDeleterImpl() { intactContext = IntactContext.getCurrentInstance(); }
public TransactionStatus beginTransaction(String transactionName) { return beginTransaction( TransactionDefinition.PROPAGATION_REQUIRES_NEW, transactionName); }
private void createDefaultUsers() { User admin = new User( "admin", "Admin", "N/A", "intact-admin@ebi.ac.uk" ); admin.setPassword("d033e22ae348aeb5660fc2140aec35850c4da997"); createAdminUser(admin); // Make the default user an admin if it does not exist User user = intactContext.getUserContext().getUser(); if (user != null) { createAdminUser(user); } }
public PsiExchangeImpl(IntactContext intactContext) { this.intactContext = intactContext; this.corePersister = intactContext.getCorePersister(); this.xmlForm = PsimiXmlForm.FORM_COMPACT; this.psiVersion = PsimiXmlVersion.VERSION_254; }
/** * Initializes a standalone context. */ public static void initContext(String[] configurationResourcePaths) { initContext(configurationResourcePaths, null); }
@Override public String toString() { return getFqn(); } }
protected DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); } }
public static DaoFactory getCurrentInstance( IntactContext context ) { return context.getDataContext().getDaoFactory(); }
private void createDefaultUsers() { User admin = new User( "admin", "Admin", "N/A", "intact-admin@ebi.ac.uk" ); admin.setPassword("d033e22ae348aeb5660fc2140aec35850c4da997"); createAdminUser(admin); // Make the default user an admin if it does not exist User user = intactContext.getUserContext().getUser(); if (user != null) { createAdminUser(user); } }
/** * Initializes a standalone context. */ public static void initContext(String[] configurationResourcePaths) { initContext(configurationResourcePaths, null); }
/** * Initializes a standalone {@code IntactContext} using a memory database. */ public static void initStandaloneContextInMemory() { initStandaloneContextInMemory((ApplicationContext) null); }
@Override public String toString() { return getFqn(); } }
public SearchableDao getDao() { if (searchableDao == null) { searchableDao = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getSearchableDao(); } return searchableDao; }
private List<Publication> getPublicationsContainingComponents(Collection<String> intactAccession) throws DatasetException { // get the intact datacontext and daofactory final DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); final DaoFactory daoFactory = dataContext.getDaoFactory(); // This query is looking for all experiences with at least one interaction involving the component of interest String componentQuery = "select i.ac from InteractionImpl i join i.components as c " + "where c.ac in (:accession)"; return getPublicationsWithSpecificSelection(componentQuery, intactAccession, daoFactory); }
public SearchableDao getDao() { if (searchableDao == null) { searchableDao = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getSearchableDao(); } return searchableDao; }
private List<Publication> getPublicationsContainingProteins(Collection<String> intactAccessions) throws DatasetException { // get the intact datacontext and daofactory final DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); final DaoFactory daoFactory = dataContext.getDaoFactory(); // This query is looking for all experiences with at least one interaction involving the protein of interest String componentQuery = "select inter.ac from Component c join c.interactor as i join c.interaction as inter " + "where i.ac in (:accessionList)"; return getPublicationsWithSpecificSelection(componentQuery, intactAccessions, daoFactory); }