public Experiment createExperimentEmpty(String shortLabel, String pubId) { Experiment experiment = new Experiment(getInstitution(), shortLabel, createBioSourceRandom()); experiment.setCvInteraction(createCvObject(CvInteraction.class, CvInteraction.COSEDIMENTATION_MI_REF, CvInteraction.COSEDIMENTATION)); experiment.setCvIdentification(createCvObject(CvIdentification.class, CvIdentification.PREDETERMINED_MI_REF, CvIdentification.PREDETERMINED)); Publication publication = createPublication(pubId); publication.addExperiment(experiment); experiment.addXref(createPrimaryReferenceXref(experiment, pubId)); return experiment; }
objectToUpdate.addXref(xref);
public Experiment createExperimentEmpty(String shortLabel, String pubId) { Experiment experiment = new Experiment(getInstitution(), shortLabel, createBioSourceRandom()); experiment.setCvInteraction(createCvObject(CvInteraction.class, CvInteraction.COSEDIMENTATION_MI_REF, CvInteraction.COSEDIMENTATION)); experiment.setCvIdentification(createCvObject(CvIdentification.class, CvIdentification.PREDETERMINED_MI_REF, CvIdentification.PREDETERMINED)); Publication publication = createPublication(pubId); publication.addExperiment(experiment); experiment.addXref(createPrimaryReferenceXref(experiment, pubId)); return experiment; }
ExperimentXref xref = new ExperimentXref(experiment.getOwner(), newt, bioSourceToAdd.getTaxId(), bioSourceToAdd.getLabel(), null, targetSpeciesQualifier); experiment.addXref(xref);
public Experiment createExperimentEmpty(String shortLabel) { Experiment experiment = new Experiment(getInstitution(), shortLabel, createBioSourceRandom()); experiment.setCvInteraction(createCvObject(CvInteraction.class, CvInteraction.COSEDIMENTATION_MI_REF, CvInteraction.COSEDIMENTATION)); experiment.setCvIdentification(createCvObject(CvIdentification.class, CvIdentification.PREDETERMINED_MI_REF, CvIdentification.PREDETERMINED)); experiment.setPublication(createPublicationRandom()); experiment.addXref(createPrimaryReferenceXref(experiment, experiment.getPublication().getShortLabel())); return experiment; }
public Experiment createExperimentEmpty(String shortLabel) { Experiment experiment = new Experiment(getInstitution(), shortLabel, createBioSourceRandom()); experiment.setCvInteraction(createCvObject(CvInteraction.class, CvInteraction.COSEDIMENTATION_MI_REF, CvInteraction.COSEDIMENTATION)); experiment.setCvIdentification(createCvObject(CvIdentification.class, CvIdentification.PREDETERMINED_MI_REF, CvIdentification.PREDETERMINED)); final Publication publication = createPublicationRandom(); experiment.setPublication(publication); publication.addExperiment(experiment); experiment.addXref(createPrimaryReferenceXref(experiment, experiment.getPublication().getShortLabel())); return experiment; }
public Experiment createExperimentEmpty(String shortLabel) { Experiment experiment = new Experiment(getInstitution(), shortLabel, createBioSourceRandom()); experiment.setCvInteraction(createCvObject(CvInteraction.class, CvInteraction.COSEDIMENTATION_MI_REF, CvInteraction.COSEDIMENTATION)); experiment.setCvIdentification(createCvObject(CvIdentification.class, CvIdentification.PREDETERMINED_MI_REF, CvIdentification.PREDETERMINED)); final Publication publication = createPublicationRandom(); experiment.setPublication(publication); publication.addExperiment(experiment); experiment.addXref(createPrimaryReferenceXref(experiment, experiment.getPublication().getShortLabel())); return experiment; }
ControlledVocabularyRepository.getPrimaryXrefQualifier() ); experiment.addXref( primaryXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( primaryXref ); ControlledVocabularyRepository.getSeeAlsoXrefQualifier() ); experiment.addXref( seeAlsoXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( seeAlsoXref ); null ); experiment.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
ControlledVocabularyRepository.getPrimaryXrefQualifier() ); experiment.addXref( primaryXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( primaryXref ); ControlledVocabularyRepository.getSeeAlsoXrefQualifier() ); experiment.addXref( seeAlsoXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( seeAlsoXref ); null ); experiment.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
ControlledVocabularyRepository.getPrimaryXrefQualifier() ); experiment.addXref( primaryXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( primaryXref ); ControlledVocabularyRepository.getSeeAlsoXrefQualifier() ); experiment.addXref( seeAlsoXref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( seeAlsoXref ); null ); experiment.addXref( xref ); IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
private Publication createUnassignedPublication(Bibref bibRef, Experiment exp) { String pubId = PublicationUtils.nextUnassignedId(IntactContext.getCurrentInstance()); Publication publication = (Publication) ConversionCache.getElement("pub:"+pubId); if (publication != null) { return publication; } publication = new Publication(getInstitution(), pubId); CvDatabase pubmed = CvObjectUtils.createCvObject(getInstitution(), CvDatabase.class, CvDatabase.PUBMED_MI_REF, CvDatabase.PUBMED); CvXrefQualifier primary = CvObjectUtils.createCvObject(getInstitution(), CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE); // add unassigned as primary ref publication.addXref(new PublicationXref(getInstitution(), pubmed, pubId, primary)); // add unassigned to exeriment exp.addXref(new ExperimentXref(getInstitution(), pubmed, pubId, primary)); if (bibRef != null){ IntactConverterUtils.populateXref(bibRef.getXref(), publication, this.publicationXrefConverter); IntactConverterUtils.populateAnnotations(bibRef, publication, getInstitution(), this.annotationConverter); } IntactContext.getCurrentInstance().getLifecycleManager().getStartStatus().create(publication, "created by xml import"); ConversionCache.putElement("pub:"+pubId, publication); return publication; }