How to find name and compartment for a species?

Another request for metadata like #61
Consider:

<species metaid="_704563" id="cpep" name="Phosphoenol pyruvate" compartment="cytosol" initialConcentration="2.67">

I would like to get the compartment and name for all the species in my model.
I can get the id and the initialConcentration from prn.u0
but not sure if/how to ge tthe others.

I see the compartment is captured here:

SBMLImporter.jl/src/species.jl

Line 16 in 943a75b

compartment = specie.compartment

But I am not sure the name is at all.
And I am not sure how to get at the compartment once it is loaded.

This is also a good suggestion!

The compartment = specie.compartment is the compartment name, but, it is also part of the internal structs that I would not like to expose to the user.

The best and most consistent solution would be to set compartment as metadata to the species, and that then it would be possible to retrieve the compartment with setmetadata. However, the species metadata field seems to be less flexible than the field for a Catalyst.Reaction.

@TorkelE the following fails for me:

using Catalyst
# Create model.
t = default_t
model = @reaction_network begin
    @species S(t) [compartment="C1"]
    kB, S + E --> SE
    kD, SE --> S + E
    kP, SE --> P + E
end

Is it something I miss about setting custom metadata field for a specie?

Yes. Species metadata is a bit of a mess. It uses the symbolic variables metadata which is implemented by Symbolics.jl. here, each metadata field need a specific implementation (I think the reason is to prevent two different packages from implementing a metadata with the same name but different purposes, without that getting detected).

If you check Catalyst, you can see how e.g. the CompoundSpecies metadata is implemented. I've requested a dev doc in Symbolics describing this for a while, and at this point I might just write it myself at some point.

Then implementing a fix similar to how CompoundSpecies is handled but for compartments sounds like the best solution.

While I implement support for this (which I should get done this week), @oxinabox you can up to then use the following workaround with the help of SBML.jl to access the compartment for each model specie:

using SBML
model = readSBML(path_sbml)
# Dict with specie info. Id must be a string
model.species[id].compartment

Note that here id must be a string.

This is closed by #69

Basically, all species now get a compartment metadata field, that can be accessed via the getcompartment function, for example to now get the compartment of the first model specie do:

# Get compartment for first model specie
using SBMLImporter, Catalyst
prn, cb = load_SBML(path_SBML)
sbml_species = species(prn.rn)
c = getcompartment(sbml_species[1])

As Catalyst does not have a compartment concept yet (but would be a good idea for the future), the getcompartment currently lives in the SBMLImporter package.