/**
* Returns a collection of bounds for reactions included in the given's model metabolism. Note
* that it has to be a sum of bounds of the parent model (if the given model has a parent) and the
* bounds directly associated with current model.
*
* @param model
* @return collection of bounds for the given model
*/
Collection<EBounds> getBoundsForModel(EModel model, EntityManager em) {
if (model.getParent() == null) {
return model.getEBoundsCollection();
} else {
/*
* There are two sources of bounds for each model.
* First, we retrieve bounds that have been defined for this model
*/
List<EBounds> res1 =
em.createQuery("SELECT e FROM EBounds e WHERE e.model = :model")
.setParameter("model", model)
.getResultList();
/*
* The remaining bounds are taken from the parent model
*/
List<EBounds> res2 =
em.createQuery(
" SELECT b FROM EModel m, EBounds b WHERE "
+ " m.id = :modelID AND m.parent IS NOT NULL AND "
+ " b.model = m.parent AND NOT EXISTS (SELECT c "
+ " FROM EBounds c WHERE c.model = :model AND "
+ " b.reaction = c.reaction )")
.setParameter("modelID", model.getId())
.setParameter("model", model)
.getResultList();
res1.addAll(res2);
return res1;
}
}
/** Removes @model from database. */
public void removeModel(EModel model) {
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
EModel modelx = em.find(EModel.class, model.getId());
removeModel(em, modelx);
// !!1tu jest błąd
// Internal Exception: java.sql.SQLIntegrityConstraintViolationException: Obiekt DELETE w
// tabeli 'ETASK' spowodował naruszenie reguły ograniczającej klucz obcy 'ECOMMONRESULTSTASK'
// dla klucza (1). Instrukcja została wycofana.
em.getTransaction().commit();
} finally {
em.close();
}
}
/**
* Finds and returns @model.
*
* @return - @model
*/
public EModel getModel(EModel model) {
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
EModel modelx =
(EModel)
em.createNamedQuery("EModel.findById")
.setParameter("id", model.getId())
.setHint("eclipselink.refresh", true)
.getSingleResult();
em.getTransaction().commit();
return modelx;
} finally {
em.close();
}
}
public List<ESpecies> getSpecies(int modelId) {
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
EModel model = em.find(EModel.class, modelId);
List<ESpecies> species =
em.createQuery(
"SELECT s FROM ESpecies s, EModel m WHERE s.compartment.metabolism.id = m.metabolism.id AND m.id = :modelId")
.setParameter("modelId", model.getId())
.getResultList();
em.getTransaction().commit();
return species;
} finally {
em.close();
}
}
