private boolean hasValidPrimaryRef( DbReference primaryRef ) { if ( (primaryRef.getRefTypeAc() != null && !CvXrefQualifier.PRIMARY_REFERENCE_MI_REF.equals(primaryRef.getRefTypeAc())) || (primaryRef.getRefTypeAc() == null && !CvXrefQualifier.PRIMARY_REFERENCE.equals(primaryRef.getRefType().toLowerCase())) || (primaryRef.getDbAc() != null && !CvDatabase.PUBMED_MI_REF.equals(primaryRef.getDbAc()) && !CvDatabase.DOI_MI_REF.equals(primaryRef.getDbAc())) || (primaryRef.getDbAc() == null && !CvDatabase.PUBMED.equals(primaryRef.getDb().toLowerCase()) && !CvDatabase.DOI.equals(primaryRef.getDb().toLowerCase())) ) { return false; } return true; }
private boolean hasValidPubmedPrimaryRef( DbReference primaryRef ) { if ( (primaryRef.getRefTypeAc() != null && !CvXrefQualifier.PRIMARY_REFERENCE_MI_REF.equals(primaryRef.getRefTypeAc())) || (primaryRef.getRefTypeAc() == null && !CvXrefQualifier.PRIMARY_REFERENCE.equals(primaryRef.getRefType().toLowerCase())) || (primaryRef.getDbAc() != null && !CvDatabase.PUBMED_MI_REF.equals(primaryRef.getDbAc())) || (primaryRef.getDbAc() == null && !CvDatabase.PUBMED.equals(primaryRef.getDb().toLowerCase())) ) { return false; } return true; }
private boolean hasValidDOIPrimaryRef( DbReference primaryRef ) { if ( (primaryRef.getRefTypeAc() != null && !CvXrefQualifier.PRIMARY_REFERENCE_MI_REF.equals(primaryRef.getRefTypeAc())) || (primaryRef.getRefTypeAc() == null && !CvXrefQualifier.PRIMARY_REFERENCE.equals(primaryRef.getRefType().toLowerCase())) || (primaryRef.getDbAc() != null && !CvDatabase.DOI_MI_REF.equals(primaryRef.getDbAc())) || (primaryRef.getDbAc() == null && !CvDatabase.DOI.equals(primaryRef.getDb().toLowerCase())) ) { return false; } return true; }
private static DbReference getPrimaryReference( Collection<DbReference> dbRefs, String dbAc ) { for ( DbReference dbRef : dbRefs ) { if ( dbRef.getRefTypeAc() != null && dbRef.getRefTypeAc().equals( CvXrefQualifier.PRIMARY_REFERENCE_MI_REF ) ) { if (dbAc != null) { if (dbAc.equals(dbRef.getDbAc())) { return dbRef; } } else { return dbRef; } } } if ( dbAc == null && !dbRefs.isEmpty() ) { return dbRefs.iterator().next(); } return null; }
if ( dbRef.getRefTypeAc() != null && dbRef.getRefTypeAc().equals( CvXrefQualifier.IDENTITY_MI_REF ) ) { if ( (dbRef.getDbAc() != null && dbRef.getDbAc().equals( CvDatabase.PSI_MI_MI_REF )) || (dbRef.getDbAc() == null && dbRef.getDb().equalsIgnoreCase( CvDatabase.PSI_MI)) ) { primary = dbRef; break; if ( (dbRef.getDbAc() != null && dbRef.getDbAc().equals( CvDatabase.UNIPROT_MI_REF )) || (dbRef.getDbAc() == null && dbRef.getDb().equalsIgnoreCase( CvDatabase.UNIPROT )) ) {
/** * Collect DbReference that match the given database criteria. * * @param xref * @param name * @param miRef * @return a non null collection. */ public static Collection<DbReference> searchByDatabase( Xref xref, String name, String miRef ) { if ( name == null && miRef == null ) { throw new IllegalArgumentException( "You must give either a name of an MI reference (or both)." ); } List<DbReference> collected = new ArrayList<DbReference>( 2 ); List<DbReference> xrefs = getAllDbReferences( xref ); for ( DbReference reference : xrefs ) { if ( name != null ) { if ( name.equalsIgnoreCase( reference.getDb() ) ) { collected.add( reference ); } } else if ( miRef != null ) { if ( miRef.equalsIgnoreCase( reference.getDbAc() ) ) { collected.add( reference ); } } } return collected; }
/** * Checks if an Xref has the given PSI-MI reference * * @param xref * @param psiRef * @return */ public static boolean hasPsiId( Xref xref, String psiRef ) { if ( psiRef == null || "".equals( psiRef.trim() ) ) { throw new IllegalArgumentException( "You must give a non null/empty PSI-MI id." ); } if ( xref == null ) { return false; } List<DbReference> list = getAllDbReferences( xref ); for ( DbReference ref : list ) { if ( PSI_MI.equalsIgnoreCase( ref.getDb() ) || PSI_MI_REF.equalsIgnoreCase( ref.getDbAc() ) ) { if ( psiRef.equalsIgnoreCase( ref.getId() ) ) { log.debug( "Found Xref( psi-mi, " + psiRef + " )" ); return true; } } } return false; }
protected void fixPubmedReferenceAsIdentityToPrimaryRef(DbReference dbRef) { if (((dbRef.getDbAc() != null && CvDatabase.PUBMED_MI_REF.equals(dbRef.getDbAc())) || (dbRef.getDbAc() == null && CvDatabase.PUBMED.equals(dbRef.getDb().toLowerCase()))) && (( dbRef.getRefTypeAc() != null && CvXrefQualifier.IDENTITY_MI_REF.equals(dbRef.getRefTypeAc())) || ( dbRef.getRefTypeAc() == null && CvXrefQualifier.IDENTITY.equals(dbRef.getRefType().toLowerCase())))) { dbRef.setRefTypeAc(CvXrefQualifier.PRIMARY_REFERENCE_MI_REF); dbRef.setRefType(CvXrefQualifier.PRIMARY_REFERENCE); final ConverterMessage converterMessage = new ConverterMessage(MessageLevel.WARN, "Incorrect cross refernece to Pubmed that had qualifier 'identity'. Changed to 'primary-reference", ConverterContext.getInstance().getLocation().getCurrentLocation()); converterMessage.setAutoFixed(true); ConverterContext.getInstance().getReport().getMessages().add(converterMessage); } }
private boolean isStatusOfType( RangeStatus status, String psimiName, String psimiIdentifier ) { boolean hasMiNumber = false; if (status.getXref() != null){ if (status.getXref().getPrimaryRef() != null){ final DbReference ref = status.getXref().getPrimaryRef(); if (ref.getDbAc() != null){ if (ref.getDbAc().equals(CvDatabase.PSI_MI_MI_REF)){ hasMiNumber = true; } else if (ref.getDb().equalsIgnoreCase(CvDatabase.PSI_MI)){ hasMiNumber = true; } } } } if ( status.getXref() != null && psimiIdentifier != null && hasMiNumber) { final DbReference ref = status.getXref().getPrimaryRef(); return psimiIdentifier.equalsIgnoreCase( ref.getId() ); } else if (status.getNames() != null){ final Names names = status.getNames(); return psimiName.equalsIgnoreCase(names.getShortLabel()) || psimiName.equalsIgnoreCase(names.getFullName()); } return false; }
!sourceDatabase.getIdentifier().equals(identityRef.getDbAc())) { interactionAcsIter.remove(); break;
public psidev.psi.mi.xml254.jaxb.DbReference toJaxb( psidev.psi.mi.xml.model.DbReference mDbReference ) { if ( mDbReference == null ) { throw new IllegalArgumentException( "You must give a non null model DbReference." ); } psidev.psi.mi.xml254.jaxb.DbReference jDbReference = new psidev.psi.mi.xml254.jaxb.DbReference(); // Initialise the JAXB object reading the model // 1. set attributes jDbReference.setDb( mDbReference.getDb() ); jDbReference.setDbAc( mDbReference.getDbAc() ); jDbReference.setId( mDbReference.getId() ); jDbReference.setRefType( mDbReference.getRefType() ); jDbReference.setRefTypeAc( mDbReference.getRefTypeAc() ); jDbReference.setSecondary( mDbReference.getSecondary() ); jDbReference.setVersion( mDbReference.getVersion() ); return jDbReference; } }
public psidev.psi.mi.xml253.jaxb.DbReferenceType toJaxb( psidev.psi.mi.xml.model.DbReference mDbReference ) { if ( mDbReference == null ) { throw new IllegalArgumentException( "You must give a non null model DbReference." ); } psidev.psi.mi.xml253.jaxb.DbReferenceType jDbReference = new psidev.psi.mi.xml253.jaxb.DbReferenceType(); // Initialise the JAXB object reading the model // 1. set attributes jDbReference.setDb( mDbReference.getDb() ); jDbReference.setDbAc( mDbReference.getDbAc() ); jDbReference.setId( mDbReference.getId() ); jDbReference.setRefType( mDbReference.getRefType() ); jDbReference.setRefTypeAc( mDbReference.getRefTypeAc() ); jDbReference.setSecondary( mDbReference.getSecondary() ); jDbReference.setVersion( mDbReference.getVersion() ); return jDbReference; } }
String dbAc = psiObject.getDbAc();