Flatten CellML Models

BiVeS is able to flatten CellML models. Flatten a model means: imports defined in a model are written into this model so that it becomes a single flat file.

In most cases this is pretty straight forward, but there are some cases that needed further attention:

• if an entity, that should be imported, uses a cmeta:id equal to another entity in the model the cmeta:id attribute in the entity and the corresponding RDF description is renamed, if existent. (see renaming)
• if an entity, that should be imported because of dependency issues of another import, uses the same name as another entity in the model the entity gets renamed. (see renaming) an example for this scenario is an imported component which defines a variable V having units X while there is another units definition for X in the importing document. here we need to rename X in the imported document to Y and modify the definition of V to use Y.

Renaming procedure

(as of version 1.3)

• if str needs to be renamed we add an _imported to str
• while str_imported still needs to be renamed we iterate the alphabet and concatenate it together with an _ (str_imported_A, str_imported_B, …, str_imported_Z, str_imported_AA …) until we found a valid name