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Cycles met ids #756

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merged 3 commits into from
Nov 11, 2023
Merged

Cycles met ids #756

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ab0a17d
Use find met in model function to check for metanetx IDs
hgscott Oct 25, 2023
2be2d2f
Use try and except to catch metabolites that are missing
hgscott Oct 26, 2023
3e505ca
Add explicit exceptions
hgscott Nov 3, 2023
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10 changes: 9 additions & 1 deletion src/memote/suite/tests/test_consistency.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@

import memote.support.consistency as consistency
import memote.support.consistency_helpers as con_helpers
import memote.support.helpers as helpers
from memote.utils import annotate, get_ids, truncate, wrapper


Expand Down Expand Up @@ -153,11 +154,18 @@ def test_detect_energy_generating_cycles(model, met):

"""
ann = test_detect_energy_generating_cycles.annotation
if met not in model.metabolites:
# Test if the metabolite is present in the model.
main_comp = helpers.find_compartment_id_in_model(model, "c")
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try:
helpers.find_met_in_model(model, met, main_comp)[0]
except ValueError:
pytest.skip("Metabolite {} is not in the MetaNetX shortlist.".format(met))
except (RuntimeError, IndexError):
pytest.skip(
"This test has been skipped since metabolite {} could "
"not be found in the model.".format(met)
)
# If the metabolite is present, carry out the test.
ann["data"][met] = consistency.detect_energy_generating_cycles(model, met)
# Report the number of cycles scaled by the number of reactions.
ann["metric"][met] = len(ann["data"][met]) / len(model.reactions)
Expand Down