public <X extends Xref> X createPrimaryReferenceXref(AnnotatedObject<X,?> parent, String primaryId) { CvXrefQualifier primaryReference = createCvObject(CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE); CvDatabase pubmedDb = createCvObject(CvDatabase.class, CvDatabase.PUBMED_MI_REF, CvDatabase.PUBMED); return createXref(parent, primaryId, primaryReference, pubmedDb); }
public Component createComponentBait(Interaction interaction, Interactor interactor) { CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.BAIT_PSI_REF, CvExperimentalRole.BAIT); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }
public Component createComponentEnzymeTarget(Interactor interactor) { Interaction interaction = createInteractionDirect(); CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.ENZYME_TARGET_PSI_REF, CvExperimentalRole.ENZYME_TARGET); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }
public Feature createFeatureRandom() { CvFeatureType cvFeatureType = createCvObject(CvFeatureType.class, CvFeatureType.EXPERIMENTAL_FEATURE_MI_REF, CvFeatureType.EXPERIMENTAL_FEATURE); return createFeature(nextString("feat"), cvFeatureType); }
public Annotation createAnnotation(String annotationText, String cvTopicPrimaryId, String cvTopicShortLabel) { CvTopic cvTopic = createCvObject(CvTopic.class, cvTopicPrimaryId, cvTopicShortLabel); return createAnnotation(annotationText, cvTopic); }
public Protein createProtein(String uniprotId, String shortLabel, String geneName, BioSource bioSource) { CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.PROTEIN_MI_REF, CvInteractorType.PROTEIN); return createProtein(uniprotId, shortLabel, geneName, bioSource, intType ); }
public Component createComponentBait(Interactor interactor) { Interaction interaction = createInteractionDirect(); return createComponentBait(interaction, interactor); }
protected void commitTransaction() throws IntactTestException { if (getDataContext().isTransactionActive()) { try { getDataContext().commitTransaction(); } catch (IntactTransactionException e) { throw new IntactTestException(e); } } }
/** * Creates a schema and initialize the database */ public void createSchema() throws IntactTransactionException { createSchema(true); }
public Component createComponentEnzyme(Interactor interactor) { Interaction interaction = createInteractionDirect(); CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.ENZYME_PSI_REF, CvExperimentalRole.ENZYME); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }
public Component createComponentBait(Interaction interaction, Interactor interactor) { CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.BAIT_PSI_REF, CvExperimentalRole.BAIT); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }
public <X extends Xref> X createPrimaryReferenceXref(AnnotatedObject<X,?> parent, String primaryId) { CvXrefQualifier primaryReference = createCvObject(CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE); CvDatabase pubmedDb = createCvObject(CvDatabase.class, CvDatabase.PUBMED_MI_REF, CvDatabase.PUBMED); return createXref(parent, primaryId, primaryReference, pubmedDb); }
public Annotation createAnnotation(String annotationText, String cvTopicPrimaryId, String cvTopicShortLabel) { CvTopic cvTopic = createCvObject(CvTopic.class, cvTopicPrimaryId, cvTopicShortLabel); return createAnnotation(annotationText, cvTopic); }
public Component createComponentEnzymeTarget(Interactor interactor) { Interaction interaction = createInteractionDirect(); CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.ENZYME_TARGET_PSI_REF, CvExperimentalRole.ENZYME_TARGET); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }
public Component createComponentPrey(Interaction interaction, Interactor interactor) { CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.PREY_PSI_REF, CvExperimentalRole.PREY); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }
public <X extends Xref> X createPrimaryReferenceXref(AnnotatedObject<X,?> parent, String primaryId) { CvXrefQualifier primaryReference = createCvObject(CvXrefQualifier.class, CvXrefQualifier.PRIMARY_REFERENCE_MI_REF, CvXrefQualifier.PRIMARY_REFERENCE); CvDatabase pubmedDb = createCvObject(CvDatabase.class, CvDatabase.PUBMED_MI_REF, CvDatabase.PUBMED); return createXref(parent, primaryId, primaryReference, pubmedDb); }
public Component createComponentEnzyme(Interactor interactor) { Interaction interaction = createInteractionDirect(); CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.ENZYME_PSI_REF, CvExperimentalRole.ENZYME); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }
public Component createComponentBait(Interaction interaction, Interactor interactor) { CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.BAIT_PSI_REF, CvExperimentalRole.BAIT); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }
public Component createComponentPrey(Interaction interaction, Interactor interactor) { CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.PREY_PSI_REF, CvExperimentalRole.PREY); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }
public Component createComponentPrey(Interaction interaction, Interactor interactor) { CvExperimentalRole expRole = createCvObject(CvExperimentalRole.class, CvExperimentalRole.PREY_PSI_REF, CvExperimentalRole.PREY); CvBiologicalRole bioRole = createCvObject(CvBiologicalRole.class, CvBiologicalRole.UNSPECIFIED_PSI_REF, CvBiologicalRole.UNSPECIFIED); return createComponent(interaction, interactor, expRole, bioRole); }