Quick speedup in loading/model_loading.py

[psalvy]

Hi there,

I just realized the way compartments were being uploaded is quite unefficient:

def loadCompartments(self, modellist, session):
    for model in modellist:
        for component in model.metabolites:
            if component.id is not None:
                if not session.query(Compartment).filter(Compartment.name == component.id[-1:len(component.id)]).count():
                    compartmentObject = Compartment(name = component.id[-1:len(component.id)])
                    session.add(compartmentObject)

This syntax generates ~1000 transactions, which takes around 5-10s
Since the number of compartments is supposedly reduced, I believe this approach might be better:

def loadCompartments(self, modellist):
        compartments_all = set()
        for model in modellist:
            for component in model.metabolites:
                if component.id is not None:
                        compartments_all.add(component.id[-1])
            for symbol in compartments_all:
                if not self.session.query(Compartment).filter(Compartment.symbol == symbol).count():
                    compartmentObject = Compartment(symbol = symbol)
                    self.session.add(compartmentObject)

This generates only as much transactions as there are compartments in a model (usually 3-5).

Anyway, it's only a static 5-10s of speed up, but over time it adds up to a lot if you do intensive testing. And it is also less stringent on your DB, if you're the DB-happiness-caring type like I am.

Best,

Pierre