private static void persistSchemaVersionIfNecessary( IntactContext context ) { IntactSession session = context.getSession(); Object obj = session.getApplicationAttribute( SCHEMA_VERSION_TO_BE_PERSISTED_FLAG ); if ( obj == null ) { return; } boolean needsToBePersisted = ( Boolean ) obj; if ( needsToBePersisted ) { persistSchemaVersion(context); session.setApplicationAttribute( SCHEMA_VERSION_TO_BE_PERSISTED_FLAG, Boolean.FALSE ); } }
private DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); } }
private DataConfig getDefaultDataConfig() { DataConfig dataConfig = RuntimeConfig.getCurrentInstance( session ).getDefaultDataConfig(); if (dataConfig == null) { dataConfig = IntactContext.calculateDefaultDataConfig( session ); } return dataConfig; } }
public static MockDaoFactory configureMockDaoFactory() { if (!IntactContext.currentInstanceExists()) { MockIntactContext.initMockContext(); } return (MockDaoFactory) IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); }
private static void initialise( ) { if ( initialisationDone == false ) { CvContext cvContext = IntactContext.getCurrentInstance().getCvContext(); // load CVs by shortlabel authorConfidenceTopic = cvContext.getByMiRef(CvTopic.class, CvTopic.AUTHOR_CONFIDENCE_MI_REF); noUniprotUpdate = cvContext.getByLabel(CvTopic.class, CvTopic.NON_UNIPROT); // load CVs by MI reference primaryReferenceXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF ); seeAlsoXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.SEE_ALSO_MI_REF ); identityXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.IDENTITY_MI_REF ); geneName = cvContext.getByMiRef(CvAliasType.class, CvAliasType.GENE_NAME_MI_REF ); initialisationDone = true; } } // init
private static void addStartAndEndPercentIfNecessary( QueryTerm term ) { if ( term.hasModifier( QueryModifier.PHRASE_DELIM ) ) { return; } String acPrefix = IntactContext.getCurrentInstance().getConfig().getAcPrefix(); if ( !term.startsWith( acPrefix ) && !term.hasModifier( QueryModifier.WILDCARD_START ) ) { term.addModifier( QueryModifier.WILDCARD_START ); } if ( !term.startsWith( acPrefix ) && !term.hasModifier( QueryModifier.WILDCARD_END ) ) { term.addModifier( QueryModifier.WILDCARD_END ); } }
public DaoFactory getDaoFactory() { DataConfig dataConfig = RuntimeConfig.getCurrentInstance( session ).getDefaultDataConfig(); return getDaoFactory( dataConfig ); }
public DaoFactory getDaoFactory( String dataConfigName ) { DataConfig dataConfig = RuntimeConfig.getCurrentInstance( session ).getDataConfig( dataConfigName ); return getDaoFactory( dataConfig ); }
private static void persistInstitutionAndCvsIfNecessary( IntactContext context ) throws IntactTransactionException { IntactSession session = context.getSession(); Object obj = session.getApplicationAttribute( INSTITUTION_TO_BE_PERSISTED_FLAG ); if ( obj == null ) { return; } boolean needsToBePersisted = ( Boolean ) obj; if ( needsToBePersisted ) { persistInstitution(context); persistBasicCvObjects(context); session.setApplicationAttribute( INSTITUTION_TO_BE_PERSISTED_FLAG, Boolean.FALSE ); } }
public static void setDryRun(IntactContext context, boolean isDryRun) { context.getSession().setAttribute(DRY_RUN_ATT, isDryRun); } }
public static boolean isInitialized( IntactSession session ) { Object obj = session.getApplicationAttribute( INITIALIZED_APP_ATT_NAME ); if ( obj == null ) { return false; } return ( Boolean ) obj; }
@Override public String toString() { return getFqn(); } }
/** * Default constructor. */ public FillPredictTables(PrintStream output) { daoFactory = IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); this.output = output; }
private static void initialise( ) { if ( initialisationDone == false ) { CvContext cvContext = IntactContext.getCurrentInstance().getCvContext(); // load CVs by shortlabel authorConfidenceTopic = cvContext.getByMiRef(CvTopic.class, CvTopic.AUTHOR_CONFIDENCE_MI_REF); noUniprotUpdate = cvContext.getByLabel(CvTopic.class, CvTopic.NON_UNIPROT); // load CVs by MI reference primaryReferenceXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF ); seeAlsoXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.SEE_ALSO_MI_REF ); identityXrefQualifier = cvContext.getByMiRef( CvXrefQualifier.class, CvXrefQualifier.IDENTITY_MI_REF ); geneName = cvContext.getByMiRef(CvAliasType.class, CvAliasType.GENE_NAME_MI_REF ); initialisationDone = true; } } // init
private DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); } }
private DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); }
private static DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); }
private static DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); }
private DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); }
private static DaoFactory getDaoFactory() { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory(); }