Lucian Smith comments

Results 113 comments of


                                            Lucian Smith

Improve flattening by testing and merging an existing fork

There are test models in the libsbml source you would be welcome to use; a few at https://github.com/sbmlteam/libsbml/tree/development/src/sbml/packages/comp/extension/test/test-data and many more at https://github.com/sbmlteam/libsbml/tree/development/src/sbml/packages/comp/util/test/test-data

🐛: Run biosimulations fails when there's multiple manifest.xml files in the archive

It's possible that the actual problem is having two manifest.xml files, which I just noticed. This seems to be something that the CombineArchiveWriter object from biosimulators_utils likes to do (which...

🐛: Run biosimulations fails when there's multiple manifest.xml files in the archive

Update: yup! When I updated the omex to remove the second manifest.xml file, it ran fine. So the bug is that it didn't report the correct failure reason.

Better error message needed than "error uploading the SED-ML specifications to the API".

[Figure3.zip](https://github.com/biosimulations/biosimulations/files/10192356/Figure3.zip) (The omex file directly, if that helps.)

Better error message needed than "error uploading the SED-ML specifications to the API".

Aha! OK, I can fix that, then. Looks like Tellurium's implementation assumed the presence of a '#', and biosimulations assumed it shouldn't be there. And I remember finding the same...

Better error message needed than "error uploading the SED-ML specifications to the API".

(the 'bug' label can be removed from this issue.)

🐛: Can't change a species value by referencing its ID

https://run.biosimulations.org/runs/63a38f3b50b2d034bd787e83#tab=log

🐛: Can't change a species value by referencing its ID

[Andrews2023_Figure5.omex.zip](https://github.com/biosimulations/biosimulations/files/10282688/Andrews2023_Figure5.omex.zip)

🐛: Can't change a species value by referencing its ID

It is indeed not an Xpath to an attribute; it's an Xpath to an element. Which is what SED-ML calls for in this situation.

🐛: Can't change a species value by referencing its ID

Quoting (again) from the spec: "In this context, a target that points to an XML element (either the target of the ComputeChange or a target of a child Variable) is...