/**
* 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;
}
}
/**
* @param parentList list of parent models
* @return list of children models
*/
public LinkedList<EModel> getChildrenByModelList(List<EModel> parentList) {
LinkedList<EModel> children = new LinkedList<EModel>();
for (EModel model : parentList) {
// children.addAll(getChildrenByModel(model));
children.addAll(model.getEModelCollection());
}
return children;
}
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();
}
}
public void addModel(
EMetabolism metabolism,
EModel model,
Map<String, ECompartment> compartment_map,
Map<String, ESpecies> species_map,
List<EReaction> reaction_list,
List<EReactant> reactant_list,
List<EProduct> product_list,
List<EBounds> bounds_list) {
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
em.persist(metabolism);
em.persist(model);
model.getMetabolism().getEModelCollection().add(model);
for (ECompartment c : compartment_map.values()) {
em.persist(c);
c.getMetabolism().getECompartmentCollection().add(c);
}
for (ESpecies sp : species_map.values()) {
em.persist(sp);
sp.getCompartment().getESpeciesCollection().add(sp);
}
for (EReaction r : reaction_list) {
em.persist(r);
r.getMetabolism().getEReactionCollection().add(r);
}
for (EReactant r : reactant_list) {
em.persist(r);
r.getSpecies().getEReactantCollection().add(r);
/* r.getReaction().getEReactantCollection().add(r); */
}
for (EProduct p : product_list) {
em.persist(p);
p.getSpecies().getEProductCollection().add(p);
/* p.getReaction().getEProductCollection().add(p); */
}
for (EBounds b : bounds_list) {
em.persist(b);
b.getModel().getEBoundsCollection().add(b);
/* b.getReaction().getEBoundsCollection().add(b); */
}
em.merge(metabolism);
em.getTransaction().commit();
} finally {
em.close();
}
}
/**
* @param modelId
* @return creactions
*/
public Collection<EReaction> getDetachedReactions(int modelId) {
ArrayList<EReaction> detachedReactions = new ArrayList<EReaction>(0);
EModel model = getModel(modelId);
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
Collection<EBounds> eboundColl = model.getEBoundsCollection();
for (EBounds bounds : eboundColl) {
if (bounds.getLowerBound() == 0 && bounds.getUpperBound() == 0) {
detachedReactions.add(bounds.getReaction());
}
}
em.getTransaction().commit();
} catch (NoResultException ex) {
em.getTransaction().rollback();
} finally {
em.close();
}
return detachedReactions;
}
/** Removes @bounds. */
public void removeBounds(EModel model) {
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
for (EBounds bounds : model.getEBoundsCollection()) {
EBounds boundsx = em.find(EBounds.class, bounds.getId());
em.remove(boundsx);
}
em.getTransaction().commit();
} finally {
em.close();
}
}
/**
* Returns list of all models from database that are ancestors of a given model (transitive
* closure version).
*
* @return - list of all ancestors of a given model (including that model).
*/
public List<EModel> getAncestorsModels(EModel start) {
EntityManager em = getEntityManager();
try {
em.getTransaction().begin();
// List<EModel> allModels = (List<EModel>) em.createQuery("select m from EModel as
// m").getResultList();
EModel model = start;
List<EModel> result = new LinkedList<EModel>();
// assume that the start model is really a model from the database
result.add(model);
// transitive closure
while (model.getParent() != null) {
result.add(model.getParent());
model = model.getParent();
}
em.getTransaction().commit();
return result;
} finally {
em.close();
}
}
/** 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();
}
}
private void removeModel(EntityManager em, EModel model) {
/* delete model's Model */
if (model.getTask() != null) {
em.remove(model.getTask());
}
/* delete children */
for (EModel child : model.getEModelCollection()) {
removeModel(em, child);
}
/* update Metabolism */
model.getMetabolism().getEModelCollection().remove(model);
if (model.getMetabolism().getEModelCollection().size() == 0) {
/* delete Metabolism */
em.remove(model.getMetabolism());
}
em.remove(model);
}
