public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, CvDatabase cvDatabase) { String dbMi = cvDatabase.getIdentifier(); return getIdentityXref(annotatedObject, dbMi); }
public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, CvDatabase cvDatabase) { String dbMi = cvDatabase.getIdentifier(); return getIdentityXref(annotatedObject, dbMi); }
public List<T> getByXref(CvDatabase database, String primaryId) { Query query = getEntityManager().createQuery("select distinct(o) from " + getEntityClass().getName() + " o inner join o.xrefs as xref " + "where xref.primaryId = :id " + " and xref.cvDatabase.identifier = :dbMi"); query.setParameter("id", primaryId); query.setParameter("dbMi", (database.getIdentifier() != null ? database.getIdentifier() : CvObjectUtils.getIdentity(database))); return query.getResultList(); }
public List<T> getByXref(CvDatabase database, String primaryId) { Query query = getEntityManager().createQuery("select distinct(o) from " + getEntityClass().getName() + " o inner join o.xrefs as xref " + "where xref.primaryId = :id " + " and xref.cvDatabase.identifier = :dbMi"); query.setParameter("id", primaryId); query.setParameter("dbMi", (database.getIdentifier() != null ? database.getIdentifier() : CvObjectUtils.getIdentity(database))); return query.getResultList(); }
public List<T> getByXrefLike(CvDatabase database, String primaryId) { Query query = getEntityManager().createQuery("select distinct(o) from " + getEntityClass().getName() + " o inner join o.xrefs as xref " + "where xref.primaryId like :id " + " and xref.cvDatabase.identifier = :dbMi"); query.setParameter("id", primaryId); query.setParameter("dbMi", (database.getIdentifier() != null ? database.getIdentifier() : CvObjectUtils.getIdentity(database))); return query.getResultList(); }
public List<T> getByXrefLike(CvDatabase database, String primaryId) { Query query = getEntityManager().createQuery("select distinct(o) from " + getEntityClass().getName() + " o inner join o.xrefs as xref " + "where xref.primaryId like :id " + " and xref.cvDatabase.identifier = :dbMi"); query.setParameter("id", primaryId); query.setParameter("dbMi", (database.getIdentifier() != null ? database.getIdentifier() : CvObjectUtils.getIdentity(database))); return query.getResultList(); }
private void prepareQuery(CvDatabase database, CvXrefQualifier qualifier, String primaryId, Query query) { query.setParameter("id", primaryId); query.setParameter("dbMi", (database.getIdentifier() != null ? database.getIdentifier() : CvObjectUtils.getIdentity(database))); query.setParameter("qualifierMi", (qualifier.getIdentifier() != null ? qualifier.getIdentifier() : CvObjectUtils.getIdentity(qualifier))); }
private void prepareQuery(CvDatabase database, CvXrefQualifier qualifier, String primaryId, Query query) { query.setParameter("id", primaryId); query.setParameter("dbMi", (database.getIdentifier() != null ? database.getIdentifier() : CvObjectUtils.getIdentity(database))); query.setParameter("qualifierMi", (qualifier.getIdentifier() != null ? qualifier.getIdentifier() : CvObjectUtils.getIdentity(qualifier))); }
public static Collection<CvObjectXref> extractIdentityXrefFrom(CvDagObject cv, String databaseId){ Collection<CvObjectXref> existingIdentities = XrefUtils.getIdentityXrefs(cv); Collection<CvObjectXref> identities = new ArrayList<CvObjectXref>(existingIdentities.size()); for (CvObjectXref ref : existingIdentities){ if (ref.getCvDatabase() != null && ref.getCvDatabase().getIdentifier().equalsIgnoreCase(databaseId)){ identities.add(ref); } } return identities; }
private static Collection<InteractorXref> extractCrossReferencesFrom(Protein protein, String databaseMiRef, String qualifierMiRef) { Collection<InteractorXref> parents = new ArrayList<InteractorXref>(); for (InteractorXref ref : protein.getXrefs()) { if (ref.getCvDatabase().getIdentifier().equals(databaseMiRef)) { if (ref.getCvXrefQualifier().getIdentifier().equals(qualifierMiRef)) { parents.add(ref); } } } return parents; }
private static Collection<InteractorXref> extractCrossReferencesFrom(Protein protein, String databaseMiRef, String qualifierMiRef) { Collection<InteractorXref> parents = new ArrayList<InteractorXref>(); for (InteractorXref ref : protein.getXrefs()) { if (ref.getCvDatabase().getIdentifier().equals(databaseMiRef)) { if (ref.getCvXrefQualifier().getIdentifier().equals(qualifierMiRef)) { parents.add(ref); } } } return parents; }
/** * Retreives Imex identifier stored in the Xrefs. * * @param interaction the interaction to search on. * @return an imex id or null if not found. */ public static String getImexIdentifier(Interaction interaction) { if (interaction == null) { throw new IllegalArgumentException("You must give a non null interaction"); } for (InteractorXref xref : interaction.getXrefs()) { if (CvDatabase.IMEX_MI_REF.equals(xref.getCvDatabase().getIdentifier())) { return xref.getPrimaryId(); } } // Could not find an IMEx id return null; }
public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, String databaseMi) { for (X xref : annotatedObject.getXrefs()) { CvXrefQualifier qualifier = xref.getCvXrefQualifier(); CvDatabase database = xref.getCvDatabase(); String qualMi; String dbMi; if (qualifier != null && database != null && (qualMi = qualifier.getIdentifier()) != null && (dbMi = database.getIdentifier()) != null && qualMi.equals(CvXrefQualifier.IDENTITY_MI_REF) && dbMi.equals(databaseMi)) { return xref; } } return null; }
public static <X extends Xref> X getIdentityXref(AnnotatedObject<X, ?> annotatedObject, String databaseMi) { for (X xref : annotatedObject.getXrefs()) { CvXrefQualifier qualifier = xref.getCvXrefQualifier(); CvDatabase database = xref.getCvDatabase(); String qualMi; String dbMi; if (qualifier != null && database != null && (qualMi = qualifier.getIdentifier()) != null && (dbMi = database.getIdentifier()) != null && qualMi.equals(CvXrefQualifier.IDENTITY_MI_REF) && dbMi.equals(databaseMi)) { return xref; } } return null; }
/** * * @param xref the xref to check * @return */ private boolean xrefPointsToOwnAc(Xref xref) { if (xref.getPrimaryId().startsWith(config.getAcPrefix())) { return true; } else { for (InstitutionXref institutionXref : IntactContext.getCurrentInstance().getInstitution().getXrefs()) { if (institutionXref.getPrimaryId().equals(xref.getCvDatabase().getIdentifier())) { return true; } } return false; } }
/** * * @param xref the xref to check * @return */ private boolean xrefPointsToOwnAc(Xref xref) { if (xref.getPrimaryId().startsWith(config.getAcPrefix())) { return true; } else { for (InstitutionXref institutionXref : IntactContext.getCurrentInstance().getInstitution().getXrefs()) { if (institutionXref.getPrimaryId().equals(xref.getCvDatabase().getIdentifier())) { return true; } } return false; } }
protected Xref getImexXref(Interaction interaction) { Collection<? extends Xref> refs; if (isCheckInitializedCollections()){ refs = IntactCore.ensureInitializedXrefs(interaction); } else { refs = interaction.getXrefs(); } for (Xref xref : refs) { if (CvDatabase.IMEX_MI_REF.equals(xref.getCvDatabase().getIdentifier()) && xref.getCvXrefQualifier() != null && CvXrefQualifier.IMEX_PRIMARY_MI_REF.equals(xref.getCvXrefQualifier().getIdentifier())) { return xref; } } return null; }
@PrePersist @PreUpdate public void prepareParentMi() { CvObject parent = (CvObject) getParent(); if (parent == null) { throw new IllegalStateException("Trying to persist or update an cv xref without parent: "+this); } if (CvXrefQualifier.IDENTITY_MI_REF.equals(getCvXrefQualifier().getIdentifier())) { if (CvDatabase.PSI_MI_MI_REF.equals(getCvDatabase().getIdentifier())) { parent.setIdentifier(getPrimaryId()); } else { if (parent.getIdentifier() == null) { parent.setIdentifier(getPrimaryId()); } } } }
@PrePersist @PreUpdate public void prepareParentMi() { CvObject parent = (CvObject) getParent(); if (parent == null) { throw new IllegalStateException("Trying to persist or update an cv xref without parent: "+this); } if (CvXrefQualifier.IDENTITY_MI_REF.equals(getCvXrefQualifier().getIdentifier())) { if (CvDatabase.PSI_MI_MI_REF.equals(getCvDatabase().getIdentifier())) { parent.setIdentifier(getPrimaryId()); } else { if (parent.getIdentifier() == null) { parent.setIdentifier(getPrimaryId()); } } } }
protected void fixPubmedReferenceAsIdentityToPrimaryRef(Xref xref) { if (CvDatabase.PUBMED_MI_REF.equals(xref.getCvDatabase().getIdentifier()) && CvXrefQualifier.IDENTITY_MI_REF.equals(xref.getCvXrefQualifier().getIdentifier())) { CvXrefQualifier primaryRef = CvObjectUtils.createCvObject(xref.getOwner(), CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE); xref.setCvXrefQualifier(primaryRef); 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); } }