public List<String> getInferredInteractions() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(inferredInteractions); query.setParameter("inferred_author", INFERRED_AUTHOR); query.setParameter("inferred_curator", CvInteraction.INFERRED_BY_CURATOR_MI_REF); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getInteractionsDrExportNotPassed() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsDrExportNotPassed); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); query.setParameter("yes", "YES"); query.setParameter("confidence", AUTHOR_SCORE_MI); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getInteractionInvolvingNonUniprotOrNonProtein() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionInvolvingNonUniprotOrNonProtein); query.setParameter("uniprot", CvDatabase.UNIPROT_MI_REF); query.setParameter("identity", CvXrefQualifier.IDENTITY_MI_REF); query.setParameter("protein", "uk.ac.ebi.intact.model.ProteinImpl"); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getInteractionsFromExperimentNoExport() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsFromExperimentNoExport); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); query.setParameter("no", "NO"); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<Object[]> getGoComponentXrefsInIntact() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsWithGoComponentXrefs); query.setParameter("go", CvDatabase.GO_MI_REF); query.setParameter("component", CvXrefQualifier.COMPONENT_MI_REF); List<Object []> xrefs = query.getResultList(); dataContext.commitTransaction(transactionStatus); return xrefs; }
public List<String> getInteractionsFromExperimentExportYes() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsFromExperimentExportYes); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); query.setParameter("yes", "YES"); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getInteractionsFromExperimentExportConditional() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsFromExperimentExportConditional); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); query.setParameter("confidence", AUTHOR_SCORE_MI); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getInteractorUniprotIdentity() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactorUniprotIdentity); query.setParameter("uniprot", CvDatabase.UNIPROT_MI_REF); query.setParameter("identity", CvXrefQualifier.IDENTITY_MI_REF); List<String> interactors = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactors; }
public List<String> getReleasedInteractions() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(releasedInteractions); query.setParameter("released", RELEASED); query.setParameter("ready_for_release", READY_FOR_RELEASE); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getInteractionsFromExperimentExportSpecified() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsFromExperimentExportSpecified); query.setParameter("drExport", CvTopic.UNIPROT_DR_EXPORT); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<Object[]> getMethodStatusInIntact() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(methodStatus); query.setParameter("export", CvTopic.UNIPROT_DR_EXPORT); List<Object []> methods = query.getResultList(); dataContext.commitTransaction(transactionStatus); return methods; }
public List<String> getInteractionsInvolvingInteractorsNoUniprotUpdate() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionsInvolvingInteractorsNoUniprotUpdate); query.setParameter("noUniprotUpdate", CvTopic.NON_UNIPROT); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getNegativeInteractions() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(negativeInteractions); query.setParameter("negative", CvTopic.NEGATIVE); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<String> getNonProteinInteractor() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(nonProteinInteractor); query.setParameter("protein", "uk.ac.ebi.intact.model.ProteinImpl"); List<String> interactors = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactors; }
/** * * @return a list of String [] which contain the intact ac and uniprot ac of each uniprot protein represented in IntAct */ private List<Object[]> getProteinsFromUniprotInIntact(){ DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus status = dataContext.beginTransaction(); String finalQuery = "select p.ac, x.primaryId from ProteinImpl p join p.xrefs as x where x.cvDatabase.identifier = :uniprot and x.cvXrefQualifier.identifier = :identity"; // create the query final Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(finalQuery); // set the query parameters query.setParameter("uniprot", CvDatabase.UNIPROT_MI_REF); query.setParameter("identity", CvXrefQualifier.IDENTITY_MI_REF); // get the intact proteins matching the cross reference List<Object[]> listOfAcs = query.getResultList(); dataContext.commitTransaction(status); return listOfAcs; }
public List<String> getInteractionInvolvedInComponents() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createQuery(interactionInvolvedInComponents); List<String> interactions = query.getResultList(); dataContext.commitTransaction(transactionStatus); return interactions; }
public List<Object[]> getTranscriptsWithDifferentParents() { DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); Query query = IntactContext.getCurrentInstance().getDaoFactory().getEntityManager().createNativeQuery(isoformsWithDifferentParents); List<Object []> methods = query.getResultList(); dataContext.commitTransaction(transactionStatus); return methods; }
/** * Search the IntAct database and retreive a BioSource having the given taxid and no CvCellType or CvTissue. * * @param taxid a non null taxid. * @return a BioSource or null if none is found. */ private BioSource searchIntactByTaxid(String taxid) throws BioSourceServiceException { log.debug("Searching in the database for BioSource(" + taxid + ")"); DataContext dataContext = IntactContext.getCurrentInstance().getDataContext(); TransactionStatus transactionStatus = dataContext.beginTransaction(); BioSourceDao bsDao = dataContext.getDaoFactory().getBioSourceDao(); BioSource biosource = bsDao.getByTaxonIdUnique(taxid); try { dataContext.commitTransaction(transactionStatus); } catch (IntactTransactionException e) { throw new BioSourceServiceException("Problem committing", e); } if (log.isDebugEnabled()) { if (biosource == null) { log.debug("Could not find Biosource having taxid: " + taxid); } else { log.debug("Found 1 biosource: " + biosource.getShortLabel() + " [" + biosource.getAc() + "]"); } } return biosource; }
/** * Filter the binary interactions of a given list of interactions and return a list composed with only binary interactions * @param interactionAcs : the list of interaction accessions * @param eligibleInteractions : the list of eligible interactions for uniprot export */ private void filterTrueBinaryInteractions(List<String> interactionAcs, List<String> eligibleInteractions) { // process each interaction of the list final int interactionCount = interactionAcs.size(); for (int i = 0; i < interactionCount; i++) { TransactionStatus status = IntactContext.getCurrentInstance().getDataContext().beginTransaction(); // get the IntAct interaction object String interactionAc = interactionAcs.get(i); Interaction interaction = IntactContext.getCurrentInstance().getDaoFactory().getInteractionDao().getByAc(interactionAc); // the interaction exists in IntAct if (interaction != null){ logger.info("\t\t Interaction: Shortlabel:" + interaction.getShortLabel() + " AC: " + interaction.getAc()); if (InteractionUtils.isBinaryInteraction(interaction)){ eligibleInteractions.add(interactionAc); } } IntactContext.getCurrentInstance().getDataContext().commitTransaction(status); } // i }
/** * Imports a stream containing PSI XML * * @param psiXmlStream the stream to read and import * @return report of the import * * @throws PersisterException thrown if there are problems parsing the stream or persisting the data in the intact-model database */ public PersisterStatistics importIntoIntact(InputStream psiXmlStream) throws PersisterException { final List<IndexedEntry> indexedEntries; try { PsimiXmlLightweightReader reader = new PsimiXmlLightweightReader( psiXmlStream ); indexedEntries = reader.getIndexedEntries(); } catch (PsimiXmlReaderException e) { throw new PsiEnricherException("Problem reading source PSI", e); } PersisterStatistics stats = new PersisterStatistics(); for (IndexedEntry indexedEntry : indexedEntries) { final TransactionStatus transactionStatus = IntactContext.getCurrentInstance().getDataContext().beginTransaction(TransactionDefinition.PROPAGATION_REQUIRES_NEW); PersisterStatistics localStats = importIntoIntact(indexedEntry); stats = merge(stats, localStats); IntactContext.getCurrentInstance().getDataContext().commitTransaction(transactionStatus); } return stats; }