private Complex createComplex(Set<? extends Entity> participants, Object... psimiIds) { Complex toReturn = bpModel.addNew(Complex.class, genUri(Complex.class, psimiIds)); if (participants != null && !participants.isEmpty()) { for (Entity participant : participants) { toReturn.addComponent((PhysicalEntity)participant); } } return toReturn; }
private UnificationXref unificationXref(String db, String id) { if(db == null || db.trim().isEmpty()) { LOG.warn("unificationXref(), db is null, id=" + id); return null; } db = dbQuickFix(db); if(id == null || id.trim().isEmpty() || BAD_ID_VALS.contains(id.trim().toUpperCase())) { LOG.warn("unificationXref(), illegal or empty id:" + id); return null; } id = id.trim(); String xuri = xmlBase + "UnificationXref_" + encode(db.toLowerCase() + "_" + id); UnificationXref x = (UnificationXref) bpModel.getByID(xuri); if(x==null) { x= bpModel.addNew(UnificationXref.class, xuri); x.setDb(db); x.setId(id); } return x; }
private PublicationXref publicationXref(String db, String id) { if(db == null || db.isEmpty()) { LOG.warn("publicationXref(), db is null, id=" + id); return null; } db = dbQuickFix(db); if(id == null || id.trim().isEmpty() || BAD_ID_VALS.contains(id.trim().toUpperCase())) { LOG.warn("publicationXref(), skip illegal id=" + id); return null; } id = id.trim(); //add only if it's a valid PMID, and not the default (IntAct) one if(("pubmed".equalsIgnoreCase(db) && !id.matches("\\d+")) || "14755292".equals(id)) { LOG.warn("publicationXref(), skip illegal or dummy publication id=" + id); return null; } String xuri = xmlBase + "PublicationXref_" + encode(db.toLowerCase() + "_" + id); PublicationXref x = (PublicationXref) bpModel.getByID(xuri); if(x==null) { x= bpModel.addNew(PublicationXref.class, xuri); x.setDb(db); x.setId(id); } return x; }
private SequenceInterval getSequenceLocation(long beginSequenceInterval, long endSequenceInterval) { SequenceInterval toReturn = bpModel.addNew(SequenceInterval.class, genUri(SequenceInterval.class, beginSequenceInterval,endSequenceInterval)); SequenceSite bpSequenceSiteBegin = bpModel.addNew(SequenceSite.class, genUri(SequenceSite.class, beginSequenceInterval)); bpSequenceSiteBegin.setSequencePosition((int) beginSequenceInterval); toReturn.setSequenceIntervalBegin(bpSequenceSiteBegin); SequenceSite bpSequenceSiteEnd = bpModel.addNew(SequenceSite.class, genUri(SequenceSite.class, endSequenceInterval)); bpSequenceSiteEnd.setSequencePosition((int) endSequenceInterval); toReturn.setSequenceIntervalEnd(bpSequenceSiteEnd); return toReturn; }
private GeneticInteraction createGeneticInteraction( Set<? extends Entity> participants, Set<InteractionVocabulary> interactionVocabularies, Object... psimiIds) { GeneticInteraction toReturn = bpModel.addNew(GeneticInteraction.class, genUri(GeneticInteraction.class, psimiIds)); if (participants != null && !participants.isEmpty()) { for (Entity participant : participants) { toReturn.addParticipant((Gene)participant); } } for(InteractionVocabulary iv : interactionVocabularies) { toReturn.addInteractionType(iv); } return toReturn; }
private MolecularInteraction createMolecularInteraction( Set<? extends Entity> participants, Set<InteractionVocabulary> interactionVocabularies, Object... psimiIds) { MolecularInteraction toReturn = bpModel.addNew(MolecularInteraction.class, genUri(MolecularInteraction.class, psimiIds)); if (participants != null && !participants.isEmpty()) { for (Entity participant : participants) { toReturn.addParticipant(participant); } } for(InteractionVocabulary iv : interactionVocabularies) { toReturn.addInteractionType(iv); } return toReturn; }
private Score createScore(String value, Set<? extends Xref> bpXrefs, Set<String> comments) { Score bpScore = bpModel.addNew(Score.class, genUri(Score.class, value)); if (value != null) { bpScore.setValue(value); } if (bpXrefs != null && !bpXrefs.isEmpty()) { for (Xref xref : bpXrefs) { bpScore.addXref(xref); } } if (comments != null && !comments.isEmpty()) { for (String comment : comments) { bpScore.addComment(comment); } } return bpScore; }
x = bpModel.addNew(RelationshipXref.class, uri); x.setDb(db); x.setId(id); RelationshipTypeVocabulary rtv = (RelationshipTypeVocabulary) bpModel.getByID(cvUri); if(rtv == null) { rtv = bpModel.addNew(RelationshipTypeVocabulary.class, cvUri); rtv.addTerm(refType); if(refTypeAc != null && !refTypeAc.isEmpty()) {//null happens, e.g., for 'uniprot-removed-ac' terms... UnificationXref cvx = bpModel.addNew(UnificationXref.class, genUri(UnificationXref.class)); cvx.setDb("PSI-MI"); cvx.setId(refTypeAc);
for (Set<Interaction> ints : inters) Pathway pathway = clonedModel.addNew(Pathway.class, System.currentTimeMillis() + "PaxtoolsPatternGeneratedMatch" + (++i));
private <T extends ControlledVocabulary> T findOrCreateControlledVocabulary( String term, UnificationXref bpXref, Class<T> bpCvClass) { // generate URI String uri = xmlBase + bpCvClass.getSimpleName() + "_" + encode( (term != null && !term.isEmpty()) ? term : bpXref.getDb() + "_" + bpXref.getId() ); // look for name in our vocabulary set T toReturn = (T) bpModel.getByID(uri); if (toReturn != null) return toReturn; // create/add a new controlled vocabulary toReturn = bpModel.addNew(bpCvClass, uri); if(term!=null) toReturn.addTerm(term); toReturn.addXref(bpXref); return toReturn; }
return; //skip creating empty useless ExperimentalForm ExperimentalForm ef = bpModel.addNew(ExperimentalForm.class, genUri(ExperimentalForm.class));
entityReference = bpModel.addNew(entityReferenceClass, baseUri);
interaction.getImexId(), interaction.getId(), experimentDescription.getId()); Evidence evidence = bpModel.addNew(Evidence.class, evUri);
private <T extends EntityFeature> T getFeature(Class<T> featureClass, Feature psiFeature) T entityFeature = (T) bpModel.addNew(featureClass, entityFeatureUri);
pro = bpModel.addNew(Provenance.class, sourceUri);