AMR issues with pde petrinets

[sabinala]

When trying to use the petrinet AMRs from this directory to solve PDEs with PyCIEMSS, I found a few issues with the AMRs:

• The "header" is too far to the right, needs one less level of indentation
• The "schema" key needs to be changed from "schema_" to "schema" in line 15 here
• We need to double check which version of petrinet schema should be used (currently you're using v0.1, but I think we have up to v0.6 now)
• Cannot have null for "grounding" but it can be empty, as in "grounding": {},

P.S. there's a typo in Drisana's last name should be Mosaphir, or Iverson (Mosaphir)

[sabinala]

@danbryce After correcting the AMR issues, I'm still getting a Runtime error so I don't have results yet, but I will track down what's going on and get back to you.

[danbryce]

@sabinala Thanks for the feedback. I've updated the PR #77 to address a few of your points, summarized as follows:

• header: whitespace isn't important for json, but I've set serialization to use an indent of 4. Please let me know if I didn't catch your meaning.
• schema: fixed
• version: I believe this is the model version, not the schema version. I can modify if needed, but I verified that the instances validate using the testing infrastructure (see test subdirs and output errors #79 ).
• nulls: I've modified the serialization to avoid emitting null values.

I think most of these issues are based on how I'm generating python from the json schema and then serializing it with pydantic. It should be correct (for some definition of correct), but needed some care with the serialization flags.

[sabinala]

@danbryce Thank you. I may have misinterpreted the error message re: the header, it said something about this needing to be the first thing in the file, so as long as what follows is further indented, it should be ok.
I'll try using these AMRs again later today.

[danbryce]

@sabinala Which tool is complaining about the format? I’ve been generating the json with pydantic, based upon Python classes generated from the json schema for petrinet AMRs. The PR README links to the script used to generate the json files. The specific location is: https://github.com/siftech/funman/blob/f092804465b0665f23e587e7f5bc05689c483711/auxiliary_packages/pde2petri/src/pde2petri/generators/common.py#L107 It should be relatively painless to modify the code to deserialize the json if you working in Python. See: https://docs.pydantic.dev/latest/concepts/json/

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On Jan 18, 2024, at 10:59 AM, sabinala ***@***.***> wrote: @danbryce Thank you. I may have misinterpreted the error message re: the header, it said something about this needing to be the first thing in the file, so as long as what follows is further indented, it should be ok. I'll try using these AMRs again later today. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[sabinala]

@danbryce ok thanks, I'll take a look at that. The error is coming from PyCIEMSS when trying to read the AMR.