template_model_from_askenet_json cannot read json from AskeNetPetriNetModel #183

djinnome · 2023-06-22T16:57:04Z

Hi folks,

Trying to convert a simpler mira model to AMR:

from mira.modeling.askenet.petrinet import AskeNetPetriNetModel
import mira
import requests
url = 'https://raw.githubusercontent.com/indralab/mira/main/notebooks/evaluation_2023.01/scenario1_sir_mira.json'
res = requests.get(url)
model_json = res.json()
sir_template = mira.metamodel.TemplateModel.from_json(model_json)
sir_model = mira.modeling.Model(sir_template)

askenet = AskeNetPetriNetModel(sir_model)

I get this error:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[9], line 12
      9 sir_template = mira.metamodel.TemplateModel.from_json(model_json)
     10 sir_model = mira.modeling.Model(sir_template)
---> 12 askenet = AskeNetPetriNetModel(sir_model)
     13 sidarthe_askenet = load_petri_model(askenet.to_json())
     14 initial_state = {param: sidarthe_mira.initials[param].value for param in sidarthe_mira.initials.keys()}

File ~/Projects/Proposals/ASKEM/mira/mira/modeling/askenet/petrinet.py:103, in AskeNetPetriNetModel.__init__(self, model)
     92     obs_data = {
     93         'id': observable.observable.name,
     94         'name': observable.observable.name,
   (...)
     97             observable.observable.expression),
     98     }
     99     self.observables.append(obs_data)
    101 self.time = {
    102     'id': model.template_model.time.name,
--> 103 } if model.template_model.time else None
    105 # Transition structure
    106 # {
    107 #   "id": "t1",
   (...)
    117 #   expression_mathml
    118 # }
    119 for idx, transition in enumerate(model.transitions.values()):

AttributeError: 'TemplateModel' object has no attribute 'time'

bgyori · 2023-06-22T16:59:45Z

I think the issue here is mainly that the model you're ingesting is an older one and the representation has changed since then. For instance, the model attribute of time is a recently implemented feature. It's a bit tricky because the model JSON you are reading was for a specific evaluation scenario, and I'm not sure whether we should keep past evaluation artifacts like those static, or incrementally keep updating them as the framework changes.

djinnome · 2023-06-22T17:20:08Z

Hi @bgyori

That makes sense. We have the same issues, so we are tagging our repos for the demos and hackathons so that it is still reproducible.

Are there any mira models that can be converted to AMR?

Even the ensemble models run into the same problem.

from mira.modeling.askenet.petrinet import AskeNetPetriNetModel
import mira
import requests
url = 'https://raw.githubusercontent.com/indralab/mira/main/notebooks/ensemble/BIOMD0000000955_template_model.json'
res = requests.get(url)
model_json = res.json()
sidarthe_template = mira.metamodel.TemplateModel.from_json(model_json)
sidarthe_model = mira.modeling.Model(sidarthe_template)
askenet_sidarthe = AskeNetPetriNetModel(sidarthe_model)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[12], line 12
     10 sidarthe_template = mira.metamodel.TemplateModel.from_json(model_json)
     11 sidarthe_model = mira.modeling.Model(sidarthe_template)
---> 12 askenet_sidarthe = AskeNetPetriNetModel(sidarthe_model)

File ~/Projects/Proposals/ASKEM/mira/mira/modeling/askenet/petrinet.py:103, in AskeNetPetriNetModel.__init__(self, model)
     92     obs_data = {
     93         'id': observable.observable.name,
     94         'name': observable.observable.name,
   (...)
     97             observable.observable.expression),
     98     }
     99     self.observables.append(obs_data)
    101 self.time = {
    102     'id': model.template_model.time.name,
--> 103 } if model.template_model.time else None
    105 # Transition structure
    106 # {
    107 #   "id": "t1",
   (...)
    117 #   expression_mathml
    118 # }
    119 for idx, transition in enumerate(model.transitions.values()):

AttributeError: 'TemplateModel' object has no attribute 'time'

kkaris · 2023-06-22T17:26:23Z

I can't reproduce these errors. I'm on the latest main: 7d94ca2

bgyori · 2023-06-22T17:28:09Z

Oh I think @kkaris is right, I just looked at the code and guessed instead of testing it. It does seem to work well if you're using the latest MIRA code.

djinnome · 2023-06-22T18:44:02Z

Ah thanks! I no longer get that error when I use the latest mira.

But now when I call:

mira.sources.askenet.petrinet.template_model_from_askenet_json(askenet_sidarthe.to_json())

I get the same sympy parse error as described in #182

ValueError: Error from parse_expr with transformed code: 'Infected *lambda '


The above exception was the direct cause of the following exception:

Traceback (most recent call last):

  File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/IPython/core/interactiveshell.py:3505 in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

  Cell In[15], line 1
    mira.sources.askenet.petrinet.template_model_from_askenet_json(askenet_sidarthe.to_json())

  File ~/Projects/Proposals/ASKEM/mira/mira/sources/askenet/petrinet.py:194 in template_model_from_askenet_json
    templates.extend(transition_to_templates(rate_obj,

  File ~/Projects/Proposals/ASKEM/mira/mira/sources/askenet/petrinet.py:259 in transition_to_templates
    rate_law = sympy.parse_expr(rate_law_expression, local_dict=symbols) \

  File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1101 in parse_expr
    raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")

  File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1092 in parse_expr
    rv = eval_expr(code, local_dict, global_dict)

  File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:907 in eval_expr
    expr = eval(

  File <string>:1
    Infected *lambda
              ^
SyntaxError: invalid syntax

The same thing happens with the Zongo 2020 model for the same reason:

def convert_mira_template_to_askenet_json(url):
    res = requests.get(url)
    model_json = res.json()
    model_template = mira.metamodel.TemplateModel.from_json(model_json)
    mira_model = mira.modeling.Model(model_template)
    askenet_model = AskeNetPetriNetModel(mira_model)
    return askenet_model.to_json()

zongo_url = 'https://raw.githubusercontent.com/indralab/mira/main/notebooks/ensemble/BIOMD0000000983_template_model.json'
askenet_json = convert_mira_template_to_askenet_json(zongo_url)
template_from_askenet = mira.sources.askenet.petrinet.template_model_from_askenet_json(askenet_json)

ValueError: Error from parse_expr with transformed code: 'Quarantined *lambda *theta '


The above exception was the direct cause of the following exception:

Traceback (most recent call last):

  File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/IPython/core/interactiveshell.py:3505 in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

  Cell In[21], line 3
    template_from_askenet = mira.sources.askenet.petrinet.template_model_from_askenet_json(askenet_json)

  File ~/Projects/Proposals/ASKEM/mira/mira/sources/askenet/petrinet.py:194 in template_model_from_askenet_json
    templates.extend(transition_to_templates(rate_obj,

  File ~/Projects/Proposals/ASKEM/mira/mira/sources/askenet/petrinet.py:259 in transition_to_templates
    rate_law = sympy.parse_expr(rate_law_expression, local_dict=symbols) \

  File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1101 in parse_expr
    raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")

  File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1092 in parse_expr
    rv = eval_expr(code, local_dict, global_dict)

  File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:907 in eval_expr
    expr = eval(

  File <string>:1
    Quarantined *lambda *theta
                 ^
SyntaxError: invalid syntax

Obviously both of these are sympy parse errors based on the reserved word lambda, but when I try to run it with the Paiva2020 model, I get a different error:

Paiva2020_url = 'https://raw.githubusercontent.com/indralab/mira/main/notebooks/ensemble/BIOMD0000000960_template_model.json'

askenet_json = convert_mira_template_to_askenet_json(Paiva2020_url)
template_from_askenet = mira.sources.askenet.petrinet.template_model_from_askenet_json(askenet_json)

---------------------------------------------------------------------------
ValidationError                           Traceback (most recent call last)
Cell In[22], line 4
      1 Paiva2020_url = 'https://raw.githubusercontent.com/indralab/mira/main/notebooks/ensemble/BIOMD0000000960_template_model.json'
      3 askenet_json = convert_mira_template_to_askenet_json(Paiva2020_url)
----> 4 template_from_askenet = mira.sources.askenet.petrinet.template_model_from_askenet_json(askenet_json)

File ~/Projects/Proposals/ASKEM/mira/mira/sources/askenet/petrinet.py:103, in template_model_from_askenet_json(model_json)
    101 mira_parameters = {}
    102 for parameter in ode_semantics.get('parameters', []):
--> 103     mira_parameters[parameter['id']] = parameter_to_mira(parameter)
    104     symbols[parameter['id']] = sympy.Symbol(parameter['id'])
    106 param_values = {
    107     p['id']: p['value'] for p in ode_semantics.get('parameters', [])
    108 }

File ~/Projects/Proposals/ASKEM/mira/mira/sources/askenet/petrinet.py:250, in parameter_to_mira(parameter)
    247 """Return a MIRA parameter from a parameter"""
    248 distr = Distribution(**parameter['distribution']) \
    249     if parameter.get('distribution') else None
--> 250 return Parameter(name=parameter['id'],
    251                  value=parameter.get('value'),
    252                  distribution=distr)

File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/pydantic/main.py:341, in pydantic.main.BaseModel.__init__()

ValidationError: 1 validation error for Parameter
value
  none is not an allowed value (type=type_error.none.not_allowed)

djinnome · 2023-06-22T22:05:50Z

Hi folks,

Sorry for hammering you with bug reports, but I was trying to figure out a pathway to success, so I thought I would roll my own AMR file:

This AMR file was generated by hand using the mira modeling tools in this notebook:

import mira
from mira.sources.askenet.petrinet import template_model_from_askenet_json
import requests
url = 'https://raw.githubusercontent.com/ciemss/pyciemss/177-examples-for-ta2-model-representation-issues/notebook/Examples_for_TA2_Model_Representation/SIAERDH_AMR.json'
res = requests.get(url)
model_json = res.json()
model = template_model_from_askenet_json(model_json)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
ValueError: Error from parse_expr with transformed code: 'S *beta *(A +I *delta )/N '

The above exception was the direct cause of the following exception:

TypeError                                 Traceback (most recent call last)
Cell In[23], line 7
      5 res = requests.get(url)
      6 model_json = res.json()
----> 7 model = template_model_from_askenet_json(model_json)

File ~/Projects/Proposals/ASKEM/mira/mira/sources/askenet/petrinet.py:194, in template_model_from_askenet_json(model_json)
    191     output_concepts = [concepts[i] for i in outputs]
    192     controller_concepts = [concepts[i] for i in controllers]
--> 194     templates.extend(transition_to_templates(rate_obj,
    195                                              input_concepts,
    196                                              output_concepts,
    197                                              controller_concepts,
    198                                              symbols))
    200 # Finally, we gather some model-level annotations
    201 name = model_json.get('name')

File ~/Projects/Proposals/ASKEM/mira/mira/sources/askenet/petrinet.py:259, in transition_to_templates(transition_rate, input_concepts, output_concepts, controller_concepts, symbols)
    257 """Return a list of templates from a transition"""
    258 rate_law_expression = transition_rate.get('expression')
--> 259 rate_law = sympy.parse_expr(rate_law_expression, local_dict=symbols) \
    260     if rate_law_expression else None
    261 if not controller_concepts:
    262     if not input_concepts:

File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1101, in parse_expr(s, local_dict, transformations, global_dict, evaluate)
   1099 for i in local_dict.pop(null, ()):
   1100     local_dict[i] = null
-> 1101 raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")

File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1092, in parse_expr(s, local_dict, transformations, global_dict, evaluate)
   1089     code = compile(evaluateFalse(code), '<string>', 'eval')
   1091 try:
-> 1092     rv = eval_expr(code, local_dict, global_dict)
   1093     # restore neutral definitions for names
   1094     for i in local_dict.pop(null, ()):

File ~/.pyenv/versions/jz-sviivr/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:907, in eval_expr(code, local_dict, global_dict)
    901 def eval_expr(code, local_dict: DICT, global_dict: DICT):
    902     """
    903     Evaluate Python code generated by ``stringify_expr``.
    904 
    905     Generally, ``parse_expr`` should be used.
    906     """
--> 907     expr = eval(
    908         code, global_dict, local_dict)  # take local objects in preference
    909     return expr

File <string>:1

TypeError: unsupported operand type(s) for /: 'Mul' and 'function'

bgyori · 2023-06-23T00:57:24Z

I debugged this and I found that the issue is that the model doesn't seem to define N as a parameter. This causes the problem with parsing a rate law formula that involves N.

djinnome · 2023-06-25T03:16:28Z

I was able to read the SIDARTHE AMR and MIRA template models into mira by renaming lambda parameters to XXlambdaXX to avoid confusing sympy.

bgyori · 2023-06-25T17:15:47Z

That's weird, renaming shouldn't be necessary. Could you send me the code you are using to read the model?

djinnome · 2023-06-25T18:59:58Z

Here you go:

import requests
import mira
from mira.modeling.askenet.petrinet import AskeNetPetriNetModel
from mira.sources.askenet.petrinet import template_model_from_askenet_json

url = 'https://raw.githubusercontent.com/indralab/mira/main/notebooks/evaluation_2023.01/scenario2_sidarthe_mira.json'
#url = 'https://raw.githubusercontent.com/indralab/mira/main/notebooks/evaluation_2023.01/scenario1_sir_mira.json'
res = requests.get(url)
model_json = res.json()
mira_template_model = mira.metamodel.TemplateModel.from_json(model_json)
mira_model = mira.modeling.Model(mira_template_model)
askenet_model = AskeNetPetriNetModel(mira_model)
askenet_mira_template_model = template_model_from_askenet_json(askenet_model.to_json())
askenet_mira_model = mira.modeling.Model(askenet_mira_template_model)

results in:

ValueError: Error from parse_expr with transformed code: 'Infected *lambda '


The above exception was the direct cause of the following exception:

Traceback (most recent call last):

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/IPython/core/interactiveshell.py:3442 in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

  Cell In[4], line 13
    askenet_mira_template_model = template_model_from_askenet_json(askenet_model.to_json())

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/mira/sources/askenet/petrinet.py:194 in template_model_from_askenet_json
    templates.extend(transition_to_templates(rate_obj,

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/mira/sources/askenet/petrinet.py:259 in transition_to_templates
    rate_law = sympy.parse_expr(rate_law_expression, local_dict=symbols) \

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1087 in parse_expr
    raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1078 in parse_expr
    rv = eval_expr(code, local_dict, global_dict)

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:906 in eval_expr
    expr = eval(

  File <string>:1
    Infected *lambda
              ^
SyntaxError: invalid syntax

djinnome · 2023-06-25T19:01:06Z

Also:

import requests
from mira.sources.askenet.petrinet import template_model_from_askenet_json
amr_url = 'https://raw.githubusercontent.com/ciemss/pyciemss/724b848b11294c4c2c5eb6b53c3eac3670783940/test/models/AMR_examples/BIOMD0000000955_askenet.json'
res = requests.get(amr_url)
amr_model_json=res.json()
amr_model = template_model_from_askenet_json(amr_model_json)

results in:

ValueError: Error from parse_expr with transformed code: 'Infected *lambda '


The above exception was the direct cause of the following exception:

Traceback (most recent call last):

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/IPython/core/interactiveshell.py:3442 in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

  Cell In[6], line 6
    amr_model = template_model_from_askenet_json(amr_model_json)

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/mira/sources/askenet/petrinet.py:194 in template_model_from_askenet_json
    templates.extend(transition_to_templates(rate_obj,

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/mira/sources/askenet/petrinet.py:259 in transition_to_templates
    rate_law = sympy.parse_expr(rate_law_expression, local_dict=symbols) \

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1087 in parse_expr
    raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:1078 in parse_expr
    rv = eval_expr(code, local_dict, global_dict)

  File ~/.pyenv/versions/pyciemss-main/lib/python3.10/site-packages/sympy/parsing/sympy_parser.py:906 in eval_expr
    expr = eval(

  File <string>:1
    Infected *lambda
              ^
SyntaxError: invalid syntax

bgyori · 2023-06-25T19:23:19Z

@djinnome this was indeed a bug, I fixed it so if you get the latest code, the two examples above work.

djinnome · 2023-06-25T19:26:21Z

I can confirm that the two examples work in my hands

* Error: gyorilab/mira#182 * Multiple controllers are added together * still getting pydantic error * Error: gyorilab/mira#183 * added more .gitignore because of silly things like .idea * added sidarthe amr * Still can't parse SIDARTHE model using mira yet * removed offending lambda to XXlambdaXX in AMR * SIDARTHE MIRA model and SIDARTHE AMR model produce same outputs * cleaned up test_askenet to have more understandable variable names * Confirmed that all of Sabina's models can be converted to ASKEM and loaded into a ScaledBetaNoisePetriNetODESystem without errors. Next up: try to interpret the sympy rate law * AMR can have lambda and it will still pass all tests. (Mira template still needs XXlambdaXX)

* Started notebook for examples regarding TA2 issues for model validation (#178) * Started notebook for examples regarding TA2 issues for model validation * Started notebook to produce AskeNet Model Representation examples in JSON format. Note: created JSON dictionary successfully; Error creating JSON fileg * Success for SIAERDH model conversion to AMR * created AMR for Model2 from custom models (SEIARHD), see JSON file * added total_population as a parameter * Deaceased -> Deceased * Fixed a few more minor errors * added SIRHD and SEIARHDS models * added SIRHD and SEIARHDS models --------- Co-authored-by: Jeremy Zucker <[email protected]> Co-authored-by: sabinala <[email protected]> Co-authored-by: Jeremy Zucker <[email protected]> * remove .idea * gitignore * Update SEIARHD_AMR.json removed git conflicts in favor of local * Fixing issue in deriv method (#187) * Error: gyorilab/mira#182 * Multiple controllers are added together * still getting pydantic error * Error: gyorilab/mira#183 * added more .gitignore because of silly things like .idea * added sidarthe amr * Still can't parse SIDARTHE model using mira yet * removed offending lambda to XXlambdaXX in AMR * SIDARTHE MIRA model and SIDARTHE AMR model produce same outputs * cleaned up test_askenet to have more understandable variable names * Confirmed that all of Sabina's models can be converted to ASKEM and loaded into a ScaledBetaNoisePetriNetODESystem without errors. Next up: try to interpret the sympy rate law * AMR can have lambda and it will still pass all tests. (Mira template still needs XXlambdaXX) * Changes to interfaces to support data IO for TA4 (#190) * added data * added interface_utils * Added updated demo with data processing * revised interfaces with AMR * removed old file * added test for interfaces demo * added results * Add detailed docstrings for TA4 interfaces (#191) * added detailed docstrings for askem interfaces * added return description * indent error * Removed untested `add_uncertainty` from TA4 interfaces (#192) * removed add_uncertainty from TA4 interfaces, as they are not thoroughly tested * fixed test * Add parameter interventions to TA4 interfaces (#193) * first pass at adding interventions to interfaces. Incomplete formatting. * lingering notebook * adding interventions to outputs * messy but it works. * Removed test_samples_intervened_values because it compares timepoint with timepoint_id, which will not work. Added test_load_and_sample_petri_net to confirm it outputs the correct dataframe under intervention * adde expected intervened samples * added load_and_calibrate_and_sample_petri * Cleaned up demo.ipynb * Cleaned up demo.ipynb * cleaned up documentation of assign_interventions_to_timepoints --------- Co-authored-by: Jeremy Zucker <[email protected]> * End-to-end integration of ensemble modeling w/ TA4 (#194) * first pass at ensemble interface for TA4 * processed output of ensemble modeling * added ensemble calibration interface * added tests and docstrings * added timepoints to ensemble output processing * removed lingering files (#199) --------- Co-authored-by: ShantMahserejian <[email protected]> Co-authored-by: Jeremy Zucker <[email protected]> Co-authored-by: sabinala <[email protected]> Co-authored-by: Jeremy Zucker <[email protected]> Co-authored-by: Sam Witty <[email protected]>

* Error: gyorilab/mira#182 * Multiple controllers are added together * still getting pydantic error * Error: gyorilab/mira#183 * added more .gitignore because of silly things like .idea * added sidarthe amr * Still can't parse SIDARTHE model using mira yet * removed offending lambda to XXlambdaXX in AMR * SIDARTHE MIRA model and SIDARTHE AMR model produce same outputs * cleaned up test_askenet to have more understandable variable names * Confirmed that all of Sabina's models can be converted to ASKEM and loaded into a ScaledBetaNoisePetriNetODESystem without errors. Next up: try to interpret the sympy rate law * AMR can have lambda and it will still pass all tests. (Mira template still needs XXlambdaXX)

djinnome added a commit to ciemss/pyciemss that referenced this issue Jun 22, 2023

Error: gyorilab/mira#183

bd129f4

djinnome mentioned this issue Jun 22, 2023

Fixing issue in deriv method ciemss/pyciemss#187

Merged

djinnome changed the title ~~AskeNetPetriNetModel cannot read Mira model~~ template_model_from_askenet_json cannot read json from AskeNetPetriNetModel Jun 22, 2023

djinnome closed this as completed Jun 25, 2023

djinnome reopened this Jun 25, 2023

bgyori mentioned this issue Jun 25, 2023

Clean formulas when processing askenet #184

Merged

bgyori closed this as completed in #184 Jun 25, 2023

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template_model_from_askenet_json cannot read json from AskeNetPetriNetModel #183

template_model_from_askenet_json cannot read json from AskeNetPetriNetModel #183

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djinnome commented Jun 25, 2023 •

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bgyori commented Jun 25, 2023

djinnome commented Jun 25, 2023

template_model_from_askenet_json cannot read json from AskeNetPetriNetModel #183

template_model_from_askenet_json cannot read json from AskeNetPetriNetModel #183

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djinnome commented Jun 25, 2023 •

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