public static Entry createEntry(Source source, Collection<Interaction> interactions) { Entry entry = new Entry(); entry.setSource(source); for (Interaction interaction : interactions) { entry.getInteractions().add(interaction); for (ExperimentDescription expDesc : interaction.getExperiments()) { entry.getExperiments().add(expDesc); } for (Participant part : interaction.getParticipants()) { entry.getInteractors().add(part.getInteractor()); } } return entry; }
if(entry.hasAvailabilities()) { for (Availability a : entry.getAvailabilities()) if (a.hasValue()) avail.add(a.getValue()); final Provenance pro = createProvenance(entry.getSource()); for(Interaction interaction : entry.getInteractions()) { for(Participant participant : interaction.getParticipants()) { for (Interaction interaction : entry.getInteractions()) { if(!participantInteractions.contains(interaction)) {
/** * Convert network metadata to CyNetwork table data. * * @param entry */ private void mapNetworkMetaData(final Entry entry) { final CyTable networkTable = network.getDefaultNetworkTable(); final Collection<Attribute> attrs = entry.getAttributes(); final Collection<ExperimentDescription> exp = entry.getExperiments(); // TODO: this takes very long time for some data sets. //mapExperiments(exp, networkTable); // Source is always unique final Source source = entry.getSource(); mapSource(source, networkTable); entry.getAvailabilities(); }
private EntrySet mergeEntriesIfNecessary(EntrySet entrySet){ if (entrySet == null){ return null; } if (entrySet.getEntries().size() > 1){ Iterator<Entry> entryIterator = entrySet.getEntries().iterator(); Entry originalEntry = entryIterator.next(); while (entryIterator.hasNext()){ Entry newEntry = entryIterator.next(); originalEntry.getExperiments().addAll(newEntry.getExperiments()); originalEntry.getInteractors().addAll(newEntry.getInteractors()); originalEntry.getInteractions().addAll(newEntry.getInteractions()); } return new EntrySet(Arrays.asList(originalEntry), entrySet.getLevel(), entrySet.getVersion(), entrySet.getMinorVersion()); } return entrySet; }
if ( mEntry.hasSource() ) { jEntry.setSource( sourceConverter.toJaxb( mEntry.getSource() ) ); if ( mEntry.hasAvailabilities() ) { if ( jEntry.getAvailabilityList() == null ) { jEntry.setAvailabilityList( new EntryType.AvailabilityList() ); for ( Availability mAvailability : mEntry.getAvailabilities() ) { jEntry.getAvailabilityList().getAvailabilities().add( availabilityConverter.toJaxb( mAvailability ) ); if ( mEntry.hasExperiments() ) { if ( jEntry.getExperimentList() == null ) { jEntry.setExperimentList( new EntryType.ExperimentList() ); for ( psidev.psi.mi.xml.model.ExperimentDescription mExperiment : mEntry.getExperiments() ) { if (!experimentIds.contains(mExperiment.getId())) { jEntry.getExperimentList().getExperimentDescriptions().add( experimentDescriptionConverter.toJaxb( mExperiment ) ); if ( mEntry.hasInteractors() ) { if ( jEntry.getInteractorList() == null ) { jEntry.setInteractorList( new EntryType.InteractorList() ); for ( psidev.psi.mi.xml.model.Interactor mInteractor : mEntry.getInteractors() ) { if (!interactorIds.contains(mInteractor.getId())) { jEntry.getInteractorList().getInteractors().add( interactorConverter.toJaxb( mInteractor ) ); for ( Interaction mInteraction : mEntry.getInteractions() ) { if ( jEntry.getInteractionList() == null ) { jEntry.setInteractionList( new EntryType.InteractionList() );
psidev.psi.mi.xml.model.Entry mEntry = new psidev.psi.mi.xml.model.Entry(); mEntry.setSource( sourceConverter.fromJaxb( jEntry.getSource() ) ); mEntry.getAvailabilities().add( availabilityConverter.fromJaxb( jAvailability ) ); mEntry.getExperiments().add( experimentDescriptionConverter.fromJaxb( jExperiment ) ); mEntry.getInteractors().add( interactorConverter.fromJaxb( jInteractor ) ); for ( EntryType.InteractionList.Interaction jInteraction : jEntry.getInteractionList().getInteractions() ) { mEntry.getInteractions().add( interactionConverter.fromJaxb( jInteraction ) ); mEntry.getAttributes().add( attributeConverter.fromJaxb( jAttribute ) ); if (mEntry.getExperiments().isEmpty()) { for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { mEntry.getExperiments().addAll(mInteraction.getExperiments()); if (mEntry.getInteractors().isEmpty()) { for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { for (psidev.psi.mi.xml.model.Participant mParticipant : mInteraction.getParticipants()) { mEntry.getInteractors().add(mParticipant.getInteractor());
public void map() { final Collection<Entry> entries = es.getEntries(); for(Entry entry: entries) { mapNetworkMetaData(entry); mapNodes(entry.getInteractors()); mapEdges(entry.getInteractions()); } }
public IntactEntry psiToIntact(Entry psiObject) { psiStartConversion(psiObject); Institution institution = institutionConverter.psiToIntact(psiObject.getSource()); setInstitution(institution); Collection<Interaction> interactions = new ArrayList<Interaction>(); for (psidev.psi.mi.xml.model.Interaction psiInteraction : psiObject.getInteractions()) { Interaction interaction = interactionConverter.psiToIntact(psiInteraction); interactions.add(interaction); } IntactEntry ientry = new IntactEntry(interactions); ientry.setInstitution(getInstitution()); IntactConverterUtils.populateAnnotations(psiObject, ientry, institution, this.annotationConverter); if (psiObject.getSource().getReleaseDate() != null) { ientry.setReleasedDate(psiObject.getSource().getReleaseDate()); } ConversionCache.clear(); psiEndConversion(psiObject); ConverterContext.getInstance().getLocation().resetPosition(); failIfInconsistentConversion(ientry, psiObject); return ientry; }
if (entry.hasSource()) { Source source = entry.getSource(); if (source.hasNames()) { Names names = source.getNames(); log.debug("Interaction count: " + entry.getInteractions().size()); for (Interaction interaction : entry.getInteractions()) { creationDate.add(entry.getSource().getReleaseDate()); if (!creationDate.isEmpty()) { binaryInteraction.setCreationDate(creationDate); creationDate.add(entry.getSource().getReleaseDate()); if (!creationDate.isEmpty()) { binaryInteraction.setCreationDate(creationDate);
xmlEntry = new Entry(); xmlEntry.setSource(xmlSource); listXrefEntryHashMap.put(sources, xmlEntry); entry.getInteractions().addAll(interactions);
public static Collection<ExperimentDescription> nonRedundantExperimentsFromPsiEntry(Entry psiEntry) { Map<Integer,ExperimentDescription> nonRedundantExps = new HashMap<Integer,ExperimentDescription>(); if( ConverterContext.getInstance().isGenerateCompactXml() ) { for (ExperimentDescription expDesc : psiEntry.getExperiments()) { nonRedundantExps.put(expDesc.getId(), expDesc); } } else { for (psidev.psi.mi.xml.model.Interaction interaction : psiEntry.getInteractions()) { for (ExperimentDescription exp : interaction.getExperiments()) { nonRedundantExps.put(exp.getId(), exp); } } } return nonRedundantExps.values(); }
protected void failIfInconsistentConversion(IntactEntry intactEntry, Entry psiEntry) { failIfInconsistentCollectionSize("interaction", intactEntry.getInteractions(), psiEntry.getInteractions()); failIfInconsistentCollectionSize("experiment", intactEntry.getExperiments(), PsiConverterUtils.nonRedundantExperimentsFromPsiEntry(psiEntry)); failIfInconsistentCollectionSize("interactor", intactEntry.getInteractors(), PsiConverterUtils.nonRedundantInteractorsFromPsiEntry(psiEntry)); }
public DateTime getReleaseDate(Entry entry) { DateTime releaseDate = null; Source source = entry.getSource(); if (source != null) { releaseDate = new DateTime(source.getReleaseDate()); } return releaseDate; }
protected RepoEntry entryToRepoEntry(Entry entry) { RepoEntry repoEntry = new RepoEntry(); normalizeEntry(entry); String name = entry.getExperiments().iterator().next() .getBibref().getXref().getPrimaryRef().getId(); repoEntry.setPmid(name); repoEntry.setReleaseDate(PsiExchange.getReleaseDate(entry)); return repoEntry; } }
if ( mEntry.hasSource() ) { jEntry.setSource( sourceConverter.toJaxb( mEntry.getSource() ) ); if ( mEntry.hasAvailabilities() ) { if ( jEntry.getAvailabilityList() == null ) { jEntry.setAvailabilityList( new AvailabilityList() ); for ( psidev.psi.mi.xml.model.Availability mAvailability : mEntry.getAvailabilities() ) { jEntry.getAvailabilityList().getAvailabilities().add( availabilityConverter.toJaxb( mAvailability ) ); if ( mEntry.hasExperiments() && PsimiXmlForm.FORM_COMPACT == ConverterContext.getInstance().getConverterConfig().getXmlForm()) { if ( jEntry.getExperimentList() == null ) { jEntry.setExperimentList( new ExperimentDescriptionList()); for ( psidev.psi.mi.xml.model.ExperimentDescription mExperiment : mEntry.getExperiments() ) { if (!experimentIds.contains(mExperiment.getId())) { jEntry.getExperimentList().getExperimentDescriptions().add( experimentDescriptionConverter.toJaxb( mExperiment ) ); if ( mEntry.hasInteractors() && PsimiXmlForm.FORM_COMPACT == ConverterContext.getInstance().getConverterConfig().getXmlForm()) { if ( jEntry.getInteractorList() == null ) { jEntry.setInteractorList( new InteractorList() ); for ( psidev.psi.mi.xml.model.Interactor mInteractor : mEntry.getInteractors() ) { if (!interactorIds.contains(mInteractor.getId())) { jEntry.getInteractorList().getInteractors().add( interactorConverter.toJaxb( mInteractor ) ); for ( psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions() ) { if ( jEntry.getInteractionList() == null ) { jEntry.setInteractionList( new InteractionList() );
psidev.psi.mi.xml.model.Entry mEntry = new psidev.psi.mi.xml.model.Entry(); mEntry.setSource( sourceConverter.fromJaxb( jEntry.getSource() ) ); mEntry.getAvailabilities().add( availabilityConverter.fromJaxb( jAvailability ) ); mEntry.getExperiments().add( experimentDescriptionConverter.fromJaxb( jExperiment ) ); mEntry.getInteractors().add( interactorConverter.fromJaxb( jInteractor ) ); for ( Interaction jInteraction : jEntry.getInteractionList().getInteractions() ) { mEntry.getInteractions().add( interactionConverter.fromJaxb( jInteraction ) ); mEntry.getAttributes().add( attributeConverter.fromJaxb( jAttribute ) ); if (mEntry.getExperiments().isEmpty()) { List<Integer> experimentIds = new ArrayList<Integer>(); for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { for (psidev.psi.mi.xml.model.ExperimentDescription jExperiment : mInteraction.getExperiments()) { if (!experimentIds.contains(jExperiment.getId())) { mEntry.getExperiments().add(jExperiment); experimentIds.add(jExperiment.getId()); if (mEntry.getInteractors().isEmpty()) { List<Integer> participantIds = new ArrayList<Integer>(); for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) {
private void normalizeEntry(Entry entry) { if (entry.getExperiments().isEmpty()) { for (Interaction interaction : entry.getInteractions()) { interaction.getExperimentRefs().clear(); for (ExperimentDescription exp : interaction.getExperiments()) { entry.getExperiments().add(exp); interaction.getExperimentRefs().add(new ExperimentRef(exp.getId())); } } } if (entry.getInteractors().isEmpty()) { for (Interaction interaction : entry.getInteractions()) { for(Participant participant : interaction.getParticipants()) { entry.getInteractors().add(participant.getInteractor()); } } } }
private void removeInteractorRedundancy( EntrySet mEntrySet ) { if( ConverterContext.getInstance().getConverterConfig().getXmlForm() == PsimiXmlForm.FORM_COMPACT ) { for ( Entry entry : mEntrySet.getEntries() ) { Map<Interactor, Interactor> uniqueInteractors = new HashMap<Interactor, Interactor>(); for ( Interaction interaction : entry.getInteractions() ) { for ( Participant participant : interaction.getParticipants() ) { if( participant.getInteractor() != null ) { final Interactor myInteractor = participant.getInteractor(); if( uniqueInteractors.containsKey( myInteractor ) ) { final Interactor uniq = uniqueInteractors.get( myInteractor ); participant.setInteractor( uniq ); } else { uniqueInteractors.put( myInteractor, myInteractor ); } } } // participants } // interactions // if we had a compact format, we cannot remove interactor redundancy without changing the interactions // and update the interactor xref if (!uniqueInteractors.isEmpty()){ entry.getInteractors().clear(); entry.getInteractors().addAll( uniqueInteractors.keySet() ); } } // entries } // model is compact }
Institution institution; if (entry.getSource() != null) { institution = institutionConverter.psiToIntact(entry.getSource()); } else { institution = intactContext.getInstitution(); for (psidev.psi.mi.xml.model.Interaction psiInteraction : entry.getInteractions()) {
for ( Interaction interaction : entry.getInteractions() ) { System.out.println( interaction.getNames().getShortLabel() );