public void onPrePersist(Interaction objToPersist) { String shortLabel = objToPersist.getShortLabel(); String newShortLabel = InteractionUtils.syncShortLabelWithDb(shortLabel); if (!shortLabel.equals(newShortLabel)) { if (log.isDebugEnabled()) log.debug("Interaction with label '"+shortLabel+"' renamed '"+newShortLabel+"'" ); objToPersist.setShortLabel(newShortLabel); } }
public Interaction createInteraction(Component ... components) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); Experiment experiment = createExperimentEmpty(); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experiment)), cvInteractionType, intType, "temp", getInstitution()); for (Component component : components) { interaction.addComponent(component); } try { String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); } catch (Exception e) { interaction.setShortLabel("unk-unk"); } return interaction; }
public Interaction createInteraction(Component ... components) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); Experiment experiment = createExperimentEmpty(); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experiment)), cvInteractionType, null, "temp", getInstitution()); for (Component component : components) { interaction.addComponent(component); } String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); return interaction; }
public Interaction createInteraction(Component ... components) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); Experiment experiment = createExperimentEmpty(); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experiment)), cvInteractionType, intType, "temp", getInstitution()); for (Component component : components) { interaction.addComponent(component); } try { String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); } catch (Exception e) { interaction.setShortLabel("unk-unk"); } return interaction; }
public Interaction createInteraction(String ... interactorShortLabels) { Interaction interaction = createInteractionDirect(); Protein prot = null; for (String interactorShortLabel : interactorShortLabels) { prot = createDeterministicProtein(interactorShortLabel, interactorShortLabel); createComponentNeutral(interaction, prot); } if (interactorShortLabels.length == 1) { createComponentNeutral(interaction, prot); } String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); return interaction; }
public Interaction createInteractionRandomBinary() { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(createExperimentEmpty())), cvInteractionType, null, nextString("label"), getInstitution()); interaction.addComponent(createComponentBait(interaction, createProteinRandom())); interaction.addComponent(createComponentPrey(interaction, createProteinRandom())); String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); return interaction; }
public Interaction createInteraction(String ... interactorShortLabels) { Interaction interaction = createInteractionDirect(); Protein prot = null; for (String interactorShortLabel : interactorShortLabels) { prot = createDeterministicProtein(interactorShortLabel, interactorShortLabel); createComponentNeutral(interaction, prot); } if (interactorShortLabels.length == 1) { createComponentNeutral(interaction, prot); } String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); return interaction; }
public Interaction createInteraction(String ... interactorShortLabels) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(createExperimentEmpty())), cvInteractionType, null, nextString("label"), getInstitution()); for (String interactorShortLabel : interactorShortLabels) { interaction.addComponent(createComponentNeutral(interaction, createProtein("uniprotId", interactorShortLabel))); } if (interactorShortLabels.length == 1) { interaction.addComponent(createComponentNeutral(interaction, createProtein("uniprotId", interactorShortLabels[0]))); } String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); return interaction; }
public Interaction createInteractionRandomBinary(String imexId) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); Experiment experimentEmpty = createExperimentEmpty(); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experimentEmpty)), cvInteractionType, intType, nextString("label"), getInstitution()); experimentEmpty.getInteractions().add(interaction); createComponentBait(interaction, createProteinRandom()); createComponentPrey(interaction, createProteinRandom()); String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); if (imexId != null) { CvObjectBuilder cvBuilder = new CvObjectBuilder(); CvXrefQualifier idQual = cvBuilder.createIdentityCvXrefQualifier(getInstitution()); CvDatabase imexDb = createCvObject(CvDatabase.class, CvDatabase.IMEX_MI_REF, CvDatabase.IMEX); interaction.addXref(new InteractorXref(getInstitution(), imexDb, imexId, idQual)); } return interaction; }
public Interaction createInteractionRandomBinary(String imexId) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); Experiment experimentEmpty = createExperimentEmpty(); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experimentEmpty)), cvInteractionType, intType, nextString("label"), getInstitution()); experimentEmpty.getInteractions().add(interaction); createComponentBait(interaction, createProteinRandom()); createComponentPrey(interaction, createProteinRandom()); String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); if (imexId != null) { CvObjectBuilder cvBuilder = new CvObjectBuilder(); CvXrefQualifier idQual = cvBuilder.createIdentityCvXrefQualifier(getInstitution()); CvDatabase imexDb = createCvObject(CvDatabase.class, CvDatabase.IMEX_MI_REF, CvDatabase.IMEX); interaction.addXref(new InteractorXref(getInstitution(), imexDb, imexId, idQual)); } return interaction; }