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vivarium-collective / vivarium-biosimulators

A Vivarium wrapper for BioSimulators
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Ode_Fba.ipynb notebook giving error #24

Open siddharth0112358 opened 2 years ago

siddharth0112358 commented 2 years ago

I am trying to run ODE_FBA.ipynb notebook and getting following error:

cell:

ode_config = { 'biosimulator_api': 'biosimulators_tellurium', 'model_source': MILLARD2016_PATH, 'model_language': ModelLanguage.SBML.value, 'simulation': 'steady_state', 'algorithm': { 'kisao_id': 'KISAO_0000019', }, 'time_step': 0.1, }

ode_process = Biosimulator(ode_config)

Error:

ValueError Traceback (most recent call last) c:\Users\siddh\Dropbox\PC\Desktop\Bioleap\Bioleap_final_notebooks\Single_cell_equations.ipynb Cell 87' in <cell line: 14>() 2 ode_config = { 3 'biosimulator_api': 'biosimulators_tellurium', 4 'model_source': MILLARD2016_PATH, (...) 10 'time_step': 0.1, 11 } 13 # make the process ---> 14 ode_process = Biosimulator(ode_config)

c:\Users\siddh\Dropbox\PC\Desktop\Bioleap\Bioleap_final_notebooks\Single_cell_equations.ipynb Cell 75' in Biosimulator.init(self, parameters) 215 # pre-process 216 self.sed_task_config = Config( 217 **self.parameters['sed_task_config']) --> 218 self.preprocessed_task = self.preprocess_sed_task( 219 self.task, 220 self.outputs, 221 config=self.sed_task_config, 222 ) 224 #################### 225 # Port Assignments # 226 #################### 227 228 # port assignments from parameters 229 default_input_port = self.parameters['default_input_port_name']

File c:\Users\siddh\AppData\Local\Programs\Python\Python38\lib\site-packages\biosimulators_tellurium\core.py:341, in preprocess_sed_task(task, variables, config, simulator_config) 337 raise_errors_warnings(validation.validate_model_language(model.language, ModelLanguage.SBML), 338 error_summary='Language for model {} is not supported.'.format(model.id)) 339 raise_errors_warnings(validation.validate_model_change_types(model.changes, (ModelAttributeChange, )), 340 error_summary='Changes for model {} are not supported.'.format(model.id)) --> 341 raise_errors_warnings(validation.validate_model_changes(task.model), 342 error_summary='Changes for model {} are invalid.'.format(model.id)) 343 raise_errors_warnings(validation.validate_simulation_type(sim, (SteadyStateSimulation, UniformTimeCourseSimulation)), 344 error_summary='{} {} is not supported.'.format(sim.class.name, sim.id)) 345 raise_errors_warnings(validation.validate_simulation(sim), 346 error_summary='Simulation {} is invalid.'.format(sim.id))

File c:\Users\siddh\AppData\Local\Programs\Python\Python38\lib\site-packages\biosimulators_utils\utils\core.py:387, in raise_errors_warnings(errors, warnings, error_summary, warning_summary) 385 if error_summary: 386 msg = error_summary + '\n ' + msg.replace('\n', '\n ') --> 387 raise ValueError(msg)

ValueError: Changes for model model are invalid.

hmvantol commented 1 year ago

@siddharth0112358 I'm having the same issue. Did you ever find a solution?

eagmon commented 1 year ago

@siddharth0112358 @hmvantol apologies for your issue. This was an experimental notebook and I have not been checking it for a while. I'll be back at work in a couple days and can try to get it up and running again. Meanwhile, can you share the versions of the different tools in your dev environment -- in particular all of the biosimulator libraries such as biosimulator utils. It seems the model changes are not being supported, so this might be an older version of utils or something else has been changed and is no longer compatible.

hmvantol commented 1 year ago

@eagmon Thanks for your response. I actually did get the cell to run by adding 'sed_task_config': { 'VALIDATE_SEDML': False, 'VALIDATE_SEDML_MODELS': False },

I've also had to try different versions of cobra, evalidate, numpy and comment out from vivarium.core.serialize import composite_specification to get some other cells to run. 

Package                  Version
------------------------ --------------------
aiofiles                 22.1.0
aiosqlite                0.19.0
airspeed                 0.5.18
alembic                  1.10.4
amici                    0.11.21
antimony                 2.12.0.2
anyio                    3.5.0
appdirs                  1.4.4
argon2-cffi              21.3.0
argon2-cffi-bindings     21.2.0
arrow                    1.2.3
Assimulo                 3.2.9
asttokens                2.0.5
async-generator          1.10
attrs                    21.4.0
Babel                    2.12.1
backcall                 0.2.0
beautifulsoup4           4.10.0
bezier                   2021.2.12
bionetgen                0.7.2
biopython                1.79
biosimulators-amici      0.1.22
biosimulators-bionetgen  0.1.20
biosimulators-boolnet    0.1.18
biosimulators-cbmpy      0.1.15
biosimulators-cobrapy    0.1.23
biosimulators-copasi     0.1.34
biosimulators-gillespy2  0.1.37
biosimulators-ginsim     0.0.9
biosimulators-libsbmlsim 0.0.6
biosimulators-masspy     0.0.9
biosimulators-pyneuroml  0.0.16
biosimulators-pysces     0.1.25
biosimulators-rbapy      0.0.4
biosimulators-tellurium  0.1.25
biosimulators-test-suite 0.1.86
biosimulators-utils      0.1.175
biosimulators-xpp        0.0.13
bleach                   4.1.0
bokeh                    3.0.0.dev4
boolean.py               3.8
Brian2                   2.5.0.3
cachetools               5.0.0
capturer                 3.0
cbmpy                    0.7.25
cement                   3.0.6
certifi                  2021.10.8
certipy                  0.1.3
cffi                     1.15.0
chardet                  4.0.0
charset-normalizer       2.0.12
cobra                    0.26.3
colomoto-jupyter         0.8.2
colorama                 0.4.4
colorlog                 6.6.0
commonmark               0.9.1
cryptography             40.0.2
cycler                   0.11.0
Cython                   0.29.28
debugpy                  1.5.1
decorator                5.1.1
defusedxml               0.7.1
depinfo                  1.7.0
diskcache                5.4.0
distlib                  0.3.4
dnspython                2.3.0
docker                   6.0.1
entrypoints              0.4
et-xmlfile               1.1.0
evalidate                1.0.2
executing                0.8.3
fastjsonschema           2.16.3
fastobo                  0.11.1
filelock                 3.6.0
fonttools                4.29.1
fqdn                     1.5.1
future                   0.18.2
gillespy2                1.6.6
ginsim                   0.4.4
glpk                     0.4.6
graphviz                 0.19.1
greenlet                 2.0.2
h11                      0.14.0
h5py                     3.6.0
httpcore                 0.17.0
httpx                    0.24.0
humanfriendly            10.0
idna                     3.3
importlib-metadata       6.6.0
importlib-resources      5.4.0
iniconfig                1.1.1
ipykernel                6.9.1
ipyparallel              8.2.0
ipython                  8.1.0
ipython-genutils         0.2.0
isodate                  0.6.1
isoduration              20.11.0
jedi                     0.18.1
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json5                    0.9.11
jsonpointer              2.3
jsonschema               4.17.3
jupyter_client           7.4.9
jupyter_core             5.3.0
jupyter-events           0.6.3
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jupyter_server_ydoc      0.8.0
jupyter-telemetry        0.1.0
jupyter-ydoc             0.2.4
jupyterhub               4.0.0
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jupyterlab-pygments      0.1.2
jupyterlab_server        2.22.1
kisao                    2.30
kiwisolver               1.3.2
libcellml                0.2.0.dev21
libNeuroML               0.3.1
libroadrunner            2.1.3
lxml                     4.8.0
Mako                     1.2.4
MarkupSafe               2.1.0
masspy                   0.1.6
matplotlib               3.5.1
matplotlib-inline        0.1.3
matplotlib-scalebar      0.8.0
mistune                  2.0.5
modelspec                0.1.3
mpmath                   1.2.1
natsort                  8.1.0
nbclassic                0.5.5
nbclient                 0.5.11
nbconvert                7.3.1
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nest-asyncio             1.5.4
netpyne                  1.0.0.2
networkx                 2.7rc1
neuromllite              0.4.2
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nose                     1.3.7
notebook                 6.4.8
notebook_shim            0.2.3
numpy                    1.19.5
oauthlib                 3.2.2
openpyxl                 3.0.9
optlang                  1.5.2
orjson                   3.8.10
packaging                21.3
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pandas                   1.4.1
pandocfilters            1.5.0
parso                    0.8.3
pexpect                  4.8.0
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pickleshare              0.7.5
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Pint                     0.18
pip                      21.2.4
pipenv                   2022.1.8
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platformdirs             2.5.1
plotly                   5.6.0
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prometheus-client        0.13.1
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pronto                   2.4.4
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pure-eval                0.2.2
py                       1.11.0
py4j                     0.10.9.3
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pydot                    1.4.2
Pygments                 2.11.2
PyLEMS                   0.5.9
pylru                    1.2.0
pymongo                  4.3.3
pyNeuroML                0.5.20
pyomexmeta               1.2.13
pyOpenSSL                23.1.1
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PyPDF2                   3.0.1
pyrsistent               0.18.1
pysces                   1.0.1
pytest                   7.0.1
python-copasi            4.34.251
python-dateutil          2.8.2
python-json-logger       2.0.7
python-libcombine        0.2.15
python-libnuml           1.1.4
python-libsbml           5.19.2
python-libsedml          2.0.27
pytz                     2021.3
pytz-deprecation-shim    0.1.0.post0
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requests                 2.28.2
rfc3339-validator        0.1.4
rfc3986                  1.5.0
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rich                     11.2.0
rpy2                     3.4.5
rrplugins                2.0.4
ruamel.yaml              0.17.21
ruamel.yaml.clib         0.2.6
sbml2matlab              1.2.3
scipy                    1.8.0
seaborn                  0.11.2
Send2Trash               1.8.1b0
setuptools               57.5.0
simplejson               3.17.6
six                      1.16.0
smoldyn                  2.68.dev202201120519
sniffio                  1.2.0
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SQLAlchemy               2.0.10
stack-data               0.2.0
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uri-template             1.2.0
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vivarium-core            1.5.5
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ypy-websocket            0.8.2
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