Suppressing warnings when loading model from file

J P

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Jun 30, 2019, 10:36:24 AM6/30/19

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Hello,

Is there a way to suppress "logger" warnings when reading an SBML model from file? Example, "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead"-

Best regards,

Jarle P

Moritz Beber

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Jun 30, 2019, 5:16:54 PM6/30/19

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Hi,

A quick possibility is to raise the logging level to error. You can read more in the Python documentation (https://docs.python.org/3/library/logging.html?highlight=logging#module-logging).

import logging

logging.getLogger("cobra").setLevel(logging.ERROR)

Best,

Moritz

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Matthias König

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Jul 3, 2019, 3:28:35 AM7/3/19

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Hi J P,

[1] another alternative is to use the validate_sbml_model function to read the model.

This is performing additional model validations (and catches all the warnings) in the error logs (this could take a bit longer to read due to the SBML validation, but for most model this does not matter too much, especially because you read the model only once.)

from cobra.io import validate_sbml_model
model, errors = validate_sbml_model(path)

[2] another is to convert the model to SBML3FBC, i.e. get rid of the warnings by encoding the model according to latest guidelines.

The cobrapy SBML exporter is doing this automatically. So you can do:

from cobra.io import read_sbml_model, write_sbml_model
model = read_sbml_model(path)
write_sbml_model(model, path_sbml3fbc)  # stores as SBML3 + fbc
read_sbml_model(path_sbml_3fbc)  # magic, no warnings

This has the big advantage that you got rid of all the legacy encoding which should in my opinion not be used any more.

Best Matthias

On Sunday, June 30, 2019 at 11:16:54 PM UTC+2, Moritz Beber wrote:

Hi,

A quick possibility is to raise the logging level to error. You can read more in the Python documentation (https://docs.python.org/3/library/logging.html?highlight=logging#module-logging).
import logging
logging.getLogger("cobra").setLevel(logging.ERROR)
Best,
Moritz

On Sun, 2019-06-30 at 07:36 -0700, J P wrote:

Hello,

Is there a way to suppress "logger" warnings when reading an SBML model from file? Example, "Encoding OBJECTIVE_COEFFICIENT in KineticLaw is discouraged, use fbc:fluxObjective instead"-

Best regards,
Jarle P

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J P

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Oct 16, 2019, 5:31:16 PM10/16/19

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Hi,

Sorry for the late reply. Thanks to both of you for the tips. I didn't know about the function to convert the model!