@Override public void visitXref( Xref xref ) { final CvDatabase db = xref.getCvDatabase(); String mi = db.getIdentifier(); if ( mi != null ) { String key = createCvKey( db.getClass(), mi ); final CvDatabase oboTerm = ( CvDatabase ) mi2cv.get( key ); if ( oboTerm == null ) { log.warn( "Could not find xref " + db.getClass().getSimpleName() + "( " + db.getShortLabel() + " ) by MI: " + mi ); } else { xref.setCvDatabase( oboTerm ); } } final CvXrefQualifier qualifier = xref.getCvXrefQualifier(); if( qualifier != null ) { mi = qualifier.getIdentifier(); if ( mi != null ) { final String key = createCvKey( qualifier.getClass(), mi ); final CvXrefQualifier oboQualifier = ( CvXrefQualifier ) mi2cv.get( key ); if ( oboQualifier == null ) { log.warn( "Could not find qualifier " + qualifier.getClass().getSimpleName() + "( " + qualifier.getShortLabel() + " ) by MI: " + mi ); } else { xref.setCvXrefQualifier( oboQualifier ); } } } }
private <X extends Xref> X createPsiMiXref(Class<X> xrefClass, String psiMi, Institution institution) { if (xrefClass == null) { throw new NullPointerException("xrefClass"); } X xref; try { xref = xrefClass.newInstance(); } catch (Exception e) { throw new IntactException("Problems instantiating Xref of type: " + xrefClass.getName()); } xref.setOwner(institution); xref.setPrimaryId(psiMi); xref.setCvDatabase(createPsiMiCvDatabase(institution)); xref.setCvXrefQualifier(createIdentityCvXrefQualifier(institution)); return xref; }
private <X extends Xref> X createPsiMiXref(Class<X> xrefClass, String psiMi, Institution institution) { if (xrefClass == null) { throw new NullPointerException("xrefClass"); } X xref; try { xref = xrefClass.newInstance(); } catch (Exception e) { throw new IntactException("Problems instantiating Xref of type: " + xrefClass.getName()); } xref.setOwner(institution); xref.setPrimaryId(psiMi); xref.setCvDatabase(createPsiMiCvDatabase(institution)); xref.setCvXrefQualifier(createIdentityCvXrefQualifier(institution)); return xref; } }
private <X extends Xref> X createPsiMiXref(Class<X> xrefClass, String psiMi) { if (xrefClass == null) { throw new NullPointerException("xrefClass"); } X xref; try { xref = xrefClass.newInstance(); } catch (Exception e) { throw new IntactException("Problems instantiating Xref of type: " + xrefClass.getName()); } xref.setOwner(institution); xref.setPrimaryId(psiMi); xref.setCvDatabase(createCvDatabase()); xref.setCvXrefQualifier(createIdentityCvXrefQualifier()); return xref; }
private <X extends Xref> X createPsiMiXref(Class<X> xrefClass, String psiMi, Institution institution) { if (xrefClass == null) { throw new NullPointerException("xrefClass"); } X xref; try { xref = xrefClass.newInstance(); } catch (Exception e) { throw new IntactException("Problems instantiating Xref of type: " + xrefClass.getName()); } xref.setOwner(institution); xref.setPrimaryId(psiMi); xref.setCvDatabase(createPsiMiCvDatabase(institution)); xref.setCvXrefQualifier(createIdentityCvXrefQualifier(institution)); return xref; } }
private static <X extends Xref> X newXrefInstance(Class<X> xrefClass, CvDatabase db, String primaryId, String secondaryId, String dbRelease, CvXrefQualifier cvXrefQual) { X xref = null; try { xref = xrefClass.newInstance(); xref.setCvDatabase(db); xref.setPrimaryId(primaryId); xref.setSecondaryId(secondaryId); xref.setDbRelease(dbRelease); xref.setCvXrefQualifier(cvXrefQual); } catch (Exception e) { throw new PsiConversionException(e); } return xref; }
public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) { X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass()); xref.setOwner(parent.getOwner()); xref.setParent(parent); xref.setPrimaryId(primaryId); xref.setCvXrefQualifier(cvXrefQualifer); xref.setCvDatabase(cvDatabase); return xref; }
public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) { X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass()); xref.setOwner(parent.getOwner()); xref.setParent(parent); xref.setPrimaryId(primaryId); xref.setCvXrefQualifier(cvXrefQualifer); xref.setCvDatabase(cvDatabase); return xref; }
public <X extends Xref> X createXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier cvXrefQualifer, CvDatabase cvDatabase) { X xref = (X) XrefUtils.newXrefInstanceFor(parent.getClass()); xref.setOwner(parent.getOwner()); xref.setParent(parent); xref.setPrimaryId(primaryId); xref.setCvXrefQualifier(cvXrefQualifer); xref.setCvDatabase(cvDatabase); return xref; }
public static <X extends Xref> X createIdentityXref(AnnotatedObject<X, ?> parent, String primaryId, CvXrefQualifier identityQual, CvDatabase cvDatabase) { X xref = (X) newXrefInstanceFor(parent.getClass()); Institution owner = parent.getOwner(); if (owner == null) { owner = IntactContext.getCurrentInstance().getInstitution(); } xref.setOwner(owner); xref.setCvDatabase(cvDatabase); xref.setCvXrefQualifier(identityQual); xref.setPrimaryId(primaryId); xref.setParent(parent); return xref; }
public static <X extends Xref> X createIdentityXref(AnnotatedObject<X,?> parent, String primaryId, CvXrefQualifier identityQual, CvDatabase cvDatabase) { X xref = (X) newXrefInstanceFor(parent.getClass()); Institution owner = parent.getOwner(); if (owner == null) { owner = IntactContext.getCurrentInstance().getInstitution(); } xref.setOwner(owner); xref.setCvDatabase(cvDatabase); xref.setCvXrefQualifier(identityQual); xref.setPrimaryId(primaryId); xref.setParent(parent); return xref; }
public static <X extends Xref> X createIdentityXref(AnnotatedObject<X, ?> parent, String primaryId, CvXrefQualifier identityQual, CvDatabase cvDatabase) { X xref = (X) newXrefInstanceFor(parent.getClass()); Institution owner = parent.getOwner(); if (owner == null) { owner = IntactContext.getCurrentInstance().getInstitution(); } xref.setOwner(owner); xref.setCvDatabase(cvDatabase); xref.setCvXrefQualifier(identityQual); xref.setPrimaryId(primaryId); xref.setParent(parent); return xref; }
/** * Note: this does not clone the parent. * * @param xref * @return * @throws uk.ac.ebi.intact.model.clone.IntactClonerException * */ protected Xref cloneXref(Xref xref) throws IntactClonerException { if (xref == null) return null; Class clazz = CgLibUtil.removeCglibEnhanced(xref.getClass()); Xref clone = null; try { final Constructor constructor = clazz.getConstructor(); clone = (Xref) constructor.newInstance(); clonerManager.addClone(xref, clone); clone.setPrimaryId(xref.getPrimaryId()); clone.setSecondaryId(xref.getSecondaryId()); clone.setDbRelease(xref.getDbRelease()); clone.setCvDatabase(clone(xref.getCvDatabase())); clone.setCvXrefQualifier(clone(xref.getCvXrefQualifier())); } catch (Exception e) { throw new IntactClonerException("An error occured upon building a " + clazz.getSimpleName(), e); } clone.setParent(clone(xref.getParent())); return clone; }
/** * Note: this does not clone the parent. * * @param xref * @return * @throws uk.ac.ebi.intact.model.clone.IntactClonerException * */ protected Xref cloneXref(Xref xref) throws IntactClonerException { if (xref == null) return null; Class clazz = CgLibUtil.removeCglibEnhanced(xref.getClass()); Xref clone = null; try { final Constructor constructor = clazz.getConstructor(); clone = (Xref) constructor.newInstance(); clonerManager.addClone(xref, clone); clone.setPrimaryId(xref.getPrimaryId()); clone.setSecondaryId(xref.getSecondaryId()); clone.setDbRelease(xref.getDbRelease()); clone.setCvDatabase(clone(xref.getCvDatabase())); clone.setCvXrefQualifier(clone(xref.getCvXrefQualifier())); } catch (Exception e) { throw new IntactClonerException("An error occured upon building a " + clazz.getSimpleName(), e); } clone.setParent(clone(xref.getParent())); return clone; }
private Xref synchronizeXref( Xref xref, AnnotatedObject parent ) { if (xref.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getXrefDao().getByAc(xref.getAc()); } xref.setCvDatabase( synchronize( xref.getCvDatabase() ) ); xref.setCvXrefQualifier( synchronize( xref.getCvXrefQualifier() ) ); xref.setParent(parent); if (xref.getAc() == null && xref.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForXref(xref), xref); } return xref; }
private Xref synchronizeXref( Xref xref, AnnotatedObject parent ) { if (xref.getAc() != null) { return IntactContext.getCurrentInstance().getDataContext().getDaoFactory() .getXrefDao().getByAc(xref.getAc()); } xref.setCvDatabase( synchronize( xref.getCvDatabase() ) ); xref.setCvXrefQualifier( synchronize( xref.getCvXrefQualifier() ) ); xref.setParent(parent); if (xref.getAc() == null && xref.getAc() != null) { annotatedObjectsToPersist.put(keyBuilder.keyForXref(xref), xref); } return xref; }
for (Xref xref : intactObject.getXrefs()) { CvDatabase cvDb = (CvDatabase) cvPersister.syncIfTransient(xref.getCvDatabase()); xref.setCvDatabase(cvDb);