Invalid (?) mapping table entries for PySB test cases

[dweindl]

There are some new validation errors after PEtab-dev/libpetab-python#480 (ignore those from PEtab-dev/libpetab-python#495):

Invalid PEtab problem generated for petab_test_suite/petabtests/cases/v2.0.0/pysb/0010.
ERROR: `A` is used in the mapping table and referenced directly in the model `model_0`.
`B` is used in the mapping table and referenced directly in the model `model_0`. [CheckMappingTable]
Invalid PEtab problem generated for petab_test_suite/petabtests/cases/v2.0.0/pysb/0011.
ERROR: `A` is used in the mapping table and referenced directly in the model `model_0`.
`B` is used in the mapping table and referenced directly in the model `model_0`. [CheckMappingTable]
Invalid PEtab problem generated for petab_test_suite/petabtests/cases/v2.0.0/pysb/0013.
ERROR: `A` is used in the mapping table and referenced directly in the model `model_0`.
`B` is used in the mapping table and referenced directly in the model `model_0`. [CheckMappingTable]
Invalid PEtab problem generated for petab_test_suite/petabtests/cases/v2.0.0/pysb/0017.
ERROR: `A` is used in the mapping table and referenced directly in the model `model_0`.
`B` is used in the mapping table and referenced directly in the model `model_0`. [CheckMappingTable]

A and B are the names of Monomers in the PySB model. It am not sure it's well-defined whether those should or should not be allowed as petabEntityId values in the mapping table. (Monomers as such, don't really play a role at the PEtab level). Nonetheless, we might want to change the petabEntityId s in those test cases.

[FFroehlich]

There are some new validation errors after PEtab-dev/libpetab-python#480 (ignore those from PEtab-dev/libpetab-python#495):

Invalid PEtab problem generated for petab_test_suite/petabtests/cases/v2.0.0/pysb/0010.
ERROR: `A` is used in the mapping table and referenced directly in the model `model_0`.
`B` is used in the mapping table and referenced directly in the model `model_0`. [CheckMappingTable]
Invalid PEtab problem generated for petab_test_suite/petabtests/cases/v2.0.0/pysb/0011.
ERROR: `A` is used in the mapping table and referenced directly in the model `model_0`.
`B` is used in the mapping table and referenced directly in the model `model_0`. [CheckMappingTable]
Invalid PEtab problem generated for petab_test_suite/petabtests/cases/v2.0.0/pysb/0013.
ERROR: `A` is used in the mapping table and referenced directly in the model `model_0`.
`B` is used in the mapping table and referenced directly in the model `model_0`. [CheckMappingTable]
Invalid PEtab problem generated for petab_test_suite/petabtests/cases/v2.0.0/pysb/0017.
ERROR: `A` is used in the mapping table and referenced directly in the model `model_0`.
`B` is used in the mapping table and referenced directly in the model `model_0`. [CheckMappingTable]

A and B are the names of Monomers in the PySB model. It am not sure it's well-defined whether those should or should not be allowed as petabEntityId values in the mapping table. (Monomers as such, don't really play a role at the PEtab level). Nonetheless, we might want to change the petabEntityId s in those test cases.

Had a look at 0010, and I think there actually is an issue with that petab test case definition. Monomers are A_ and B_, so I don't think that's what's causing trouble. Instead, the model defines Observable("A", A_()) and Observable("B", B_()), which are exposed as petabEntityId and clash with A and B in the mapping table.

[dweindl]

Had a look at 0010, and I think there actually is an issue with that petab test case definition. Monomers are A_ and B_, so I don't think that's what's causing trouble. Instead, the model defines Observable("A", A_()) and Observable("B", B_()), which are exposed as petabEntityId and clash with A and B in the mapping table.

You are right.