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[cellml-discussion] Precise semantics of generateFlattenedModel()


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  • From: ak.miller at auckland.ac.nz (Andrew Miller)
  • Subject: [cellml-discussion] Precise semantics of generateFlattenedModel()
  • Date: Fri, 24 Feb 2006 10:37:22 +1300
Hi all,

There is currently no precise specification of the semantics for the
generateFlattenedModel() operation on the cellml_api::Model interface.

I propose the following:

Flattening CellML models:
--- The flattened model should contain:
1) Components => All components in the base model, including any
components
which have been imported into the base model. Also all components which
are connected to any component that is to be included in the flattened
model. Components in the base model shall always adopt their original
names, and components which are imported into the base model shall
always adopt the name of the ImportComponent. In all other cases, the
API implementation shall attempt to assign the preferred name according
to the following rules, but where that would result in a conflict with
another component, the CellML API shall rename the component to another
implementation defined, non-conflicting name. Such components shall
have the preferred name of the shallowest ImportComponent referring to
them, or where no such ImportComponent exists, the name of the
Component.
2) Groups => All groups containing one or more selected top-level
ComponentRefs. Selected ComponentRefs are ComponentRefs which either:
1) Have a group element as their parent, and refer to a component which
has been put into the flattened model, and have one or more
ComponentRef children which refer to a component which has been put
into the flattened model, or
2) Have a selected ComponentRef as a parent and refer to a component
which has been put into the flattened model.

The groups should refer to components by their name in the flattened
model.
3) Units => All units from any models from which any components have been
used(including those imported into such models).
Units in the base model shall always adopt their original
names, and components which are imported into the base model
shall always adopt the name of the ImportUnits. In all other
cases, the API implementation shall attempt to assign the
preferred name according to the following rules, but where
that
would result in a conflict with another units definition, the
CellML API shall rename the units definition to another
implementation defined, non-conflicting name. Such units
shall have the preferred name of the shallowest ImportUnits
referring to them, or where no such ImportUnits exists, the
name of the Units.
4) Connections => All connections which involve any component which has
been put into the flattened model.

The connections should refer to components by their name in the
flattened model.

Any other elements in the top level model from any namespace will also be
duplicated(including reactions, metadata, and extension elements), except that
import elements in either of the CellML namespaces will not be included. Only
the top-level elements from imported models mentioned in the above list will
be included. Where an element is included, all child elements will also be
included.

Opinions?

Best regards,
Andrew Miller


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