private static CvFuzzyType createCvFuzzyType(String position) { if (position == null) { throw new IllegalArgumentException("The range position cannot be null."); } for (String key : rangeStatusMap.keySet()) { if (position.toLowerCase().contains(key)) { return rangeStatusMap.get(key); } } return CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvFuzzyType.class, CvFuzzyType.CERTAIN_MI_REF, CvFuzzyType.CERTAIN); }
private static CvFuzzyType createCvFuzzyType(String position) { if (position == null) { throw new IllegalArgumentException("The range position cannot be null."); } for (String key : rangeStatusMap.keySet()) { if (position.toLowerCase().contains(key)) { return rangeStatusMap.get(key); } } return CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvFuzzyType.class, CvFuzzyType.CERTAIN_MI_REF, CvFuzzyType.CERTAIN); }
@PostConstruct private void init() { this.nonMiCvDatabase = CvObjectUtils.createCvObject( IntactContext.getCurrentInstance().getInstitution(), CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT ); }
protected InteractorXref createImexXref(Interaction interaction, String imexId) { CvDatabase cvImex = CvObjectUtils.createCvObject(interaction.getOwner(), CvDatabase.class, CvDatabase.IMEX_MI_REF, CvDatabase.IMEX); cvImex.setFullName(CvDatabase.IMEX); CvXrefQualifier imexPrimary = CvObjectUtils.createCvObject(interaction.getOwner(), CvXrefQualifier.class, CvXrefQualifier.IMEX_PRIMARY_MI_REF, CvXrefQualifier.IMEX_PRIMARY); return XrefUtils.createIdentityXref(interaction, imexId, imexPrimary, cvImex); }
public static <A extends Alias> A createAliasGeneName(AnnotatedObject<?, A> parent, String name) { CvAliasType cvGeneName = CvObjectUtils.createCvObject(parent.getOwner(), CvAliasType.class, CvAliasType.GENE_NAME_MI_REF, CvAliasType.GENE_NAME); return createAlias(parent, name, cvGeneName); }
public static <A extends Alias> A createAliasGeneName(AnnotatedObject<?,A> parent, String name) { CvAliasType cvGeneName = CvObjectUtils.createCvObject(parent.getOwner(), CvAliasType.class, CvAliasType.GENE_NAME_MI_REF, CvAliasType.GENE_NAME); return createAlias(parent, name, cvGeneName); }
protected Alias toAlias( CvObject cvobj, String aliasName ) { Institution owner = IntactContext.getCurrentInstance().getInstitution(); CvAliasType alias = getCvObjectByLabel( CvAliasType.class, CvAliasType.GO_SYNONYM ); if ( alias == null ) { if ( log.isTraceEnabled() ) log.trace( "alias ==null creating new" ); alias = CvObjectUtils.createCvObject( owner, CvAliasType.class, CvAliasType.GO_SYNONYM_MI_REF, CvAliasType.GO_SYNONYM ); } return AliasUtils.createAlias( cvobj, aliasName, alias ); }
public static <X extends Xref> X createIdentityXrefEmblGenbankDdbj(AnnotatedObject<X, ?> parent, String emblGenbankDdbjId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.DDBG_MI_REF, CvDatabase.DDBG); return createIdentityXref(parent, emblGenbankDdbjId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
private <T extends CvObject> T createCvIfMissing( Class<T> clazz, String cvId, String cvName, CvDagObject parent ) { T cv = daoFactory.getCvObjectDao(clazz).getByIdentifier(cvId); if ( cv == null) { cv = CvObjectUtils.createCvObject(configuration.getDefaultInstitution(), clazz, cvId, cvName ); corePersister.saveOrUpdate(cv); if( parent != null && cv instanceof CvDagObject ) { CvDagObject cvDag = (CvDagObject) cv; cvDag.addParent( parent ); } } return cv; }
public static <X extends Xref> X createIdentityXrefIntact(AnnotatedObject<X, ?> parent, String intactId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); return createIdentityXref(parent, intactId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefChebi(AnnotatedObject<X, ?> parent, String chebiId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.CHEBI_MI_REF, CvDatabase.CHEBI); return createIdentityXref(parent, chebiId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
private <T extends CvObject> T createCvIfMissing( Class<T> clazz, String cvId, String cvName, CvDagObject parent ) { T cv = daoFactory.getCvObjectDao(clazz).getByIdentifier(cvId); if ( cv == null) { cv = CvObjectUtils.createCvObject(configuration.getDefaultInstitution(), clazz, cvId, cvName ); corePersister.saveOrUpdate(cv); if( parent != null && cv instanceof CvDagObject ) { CvDagObject cvDag = (CvDagObject) cv; cvDag.addParent( parent ); } } return cv; }
public static <X extends Xref> X createIdentityXrefChebi(AnnotatedObject<X, ?> parent, String chebiId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.CHEBI_MI_REF, CvDatabase.CHEBI); return createIdentityXref(parent, chebiId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X, ?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.UNIPROT_MI_REF, CvDatabase.UNIPROT); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X,?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.UNIPROT_MI_REF, CvDatabase.UNIPROT); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefIntact(AnnotatedObject<X, ?> parent, String intactId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.INTACT_MI_REF, CvDatabase.INTACT); return createIdentityXref(parent, intactId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefEmblGenbankDdbj(AnnotatedObject<X, ?> parent, String emblGenbankDdbjId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.DDBG_MI_REF, CvDatabase.DDBG); return createIdentityXref(parent, emblGenbankDdbjId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
public static <X extends Xref> X createIdentityXrefUniprot(AnnotatedObject<X, ?> parent, String primaryId) { CvObjectBuilder builder = new CvObjectBuilder(); CvDatabase cvDatabase = CvObjectUtils.createCvObject(parent.getOwner(), CvDatabase.class, CvDatabase.UNIPROT_MI_REF, CvDatabase.UNIPROT); return createIdentityXref(parent, primaryId, builder.createIdentityCvXrefQualifier(parent.getOwner()), cvDatabase); }
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); } }
public static Annotation hideTerm(CvObject c, String message){ DaoFactory factory = IntactContext.getCurrentInstance().getDaoFactory(); CvTopic topicFromDb = factory.getCvObjectDao(CvTopic.class).getByShortLabel(CvTopic.HIDDEN); if (topicFromDb == null){ topicFromDb = CvObjectUtils.createCvObject(IntactContext.getCurrentInstance().getInstitution(), CvTopic.class, null, CvTopic.HIDDEN); IntactContext.getCurrentInstance().getCorePersister().saveOrUpdate(topicFromDb); } Annotation newAnnotation = new Annotation(topicFromDb, message); c.addAnnotation(newAnnotation); return newAnnotation; }