# -*- coding: utf-8 -*-
# Copyright 2017 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Syntax tests performed on an instance of ``cobra.Model``."""
from __future__ import absolute_import
import logging
import pytest
import memote.support.syntax as syntax
LOGGER = logging.getLogger(__name__)
@pytest.fixture(scope="module")
[docs]def non_cytosolic(read_only_model, store):
"""Provide all non-cytosolic compartments."""
compartments = sorted(read_only_model.compartments)
try:
store["non_cytosolic"] = compartments.remove('c')
return compartments
except ValueError:
LOGGER.error(
"The model does not contain a compartment ID labeled 'c' for the "
"cytosol which is an essential compartment. Many syntax tests "
"depend on this being labeled accordingly.")
store["non_cytosolic"] = []
return []
[docs]def test_non_transp_rxn_id_compartment_suffix_match(read_only_model, store,
non_cytosolic):
"""Expect all reactions outside of the cytosol to be tagged accordingly."""
store["reaction_compartment_suffix"] = list()
for compartment in non_cytosolic:
store["reaction_compartment_suffix"].append([
rxn.id for rxn in syntax.find_rxn_id_compartment_suffix(
read_only_model, compartment)])
for compartment, no_match_rxns in zip(non_cytosolic,
store["reaction_compartment_suffix"]):
assert len(no_match_rxns) == 0, \
"The following reactions in compartment {} are not tagged " \
"correctly: {}".format(compartment, ", ".join(no_match_rxns))
[docs]def test_non_transp_rxn_id_suffix_compartment_match(
read_only_model, store, non_cytosolic):
"""Expect compartment-tagged reactions to involve fitting metabolites."""
store["reaction_metabolite_compartment"] = list()
for compartment in non_cytosolic:
store["reaction_metabolite_compartment"].append([
rxn.id for rxn in syntax.find_rxn_id_suffix_compartment(
read_only_model, compartment)])
for compartment, mislab_rxns in zip(
non_cytosolic, store["reaction_metabolite_compartment"]):
assert len(mislab_rxns) == 0, \
"The following reactions in compartment {} are tagged to not " \
"contain metabolites from that compartment: {}"\
"".format(compartment, ", ".join(mislab_rxns))
[docs]def test_non_abc_transp_rxn_tag_match(read_only_model, store):
"""Expect all non-abc transport reactions to be tagged with a ``t``."""
store["untagged_normal_transport"] = [
rxn.id for rxn in syntax.find_reaction_tag_transporter(
read_only_model
)]
assert len(store["untagged_normal_transport"]) == 0, \
"The following non-atp transport reactions are not tagged " \
"correctly: {}".format(", ".join(store["untagged_normal_transport"]))
[docs]def test_abc_transp_rxn_tag_match(read_only_model, store):
"""Expect all abc transport reactions to be tagged with ``abc``."""
store["untagged_abc_transport"] = [
rxn.id for rxn in syntax.find_abc_tag_transporter(read_only_model)]
assert len(store["untagged_abc_transport"]) == 0, \
"The following abc transport reactions are not tagged" \
"correctly: {}".format(", ".join(store["untagged_abc_transport"]))
[docs]def test_upper_case_mets(read_only_model, store):
"""Expect all metabolites to be lower case with accepted exceptions."""
store["uppercase_metabolites"] = [
met.id for met in syntax.find_upper_case_mets(read_only_model)]
assert len(store["uppercase_metabolites"]) == 0, \
"The IDs of the following metabolites are not written in lower case" \
" {}".format(", ".join(store["uppercase_metabolites"]))
[docs]def test_demand_reaction_tag_match(read_only_model, store):
"""Expect all demand reaction IDs to be prefixed with ``DM_``."""
store["untagged_demand"] = [
rxn.id for rxn in syntax.find_untagged_demand_rxns(read_only_model)]
assert len(store["untagged_demand"]) == 0, \
"The IDs of the following demand reactions are not tagged with 'DM_'" \
" {}".format(", ".join(store["untagged_demand"]))
[docs]def test_false_demand_reaction(read_only_model, store):
"""Expect all rxns that are tagged with ``DM_`` to be true demand rxns."""
store["false_demand"] = [
rxn.id for rxn in syntax.find_false_demand_rxns(read_only_model)]
assert len(store["false_demand"]) == 0, \
"The IDs of the following reactions are falsely tagged with 'DM_'" \
" {}".format(", ".join(store["false_demand"]))
[docs]def test_sink_reaction_tag_match(read_only_model, store):
"""Expect all sink reaction IDs to be prefixed with ``SK_``."""
store["untagged_sink"] = [
rxn.id for rxn in syntax.find_untagged_sink_rxns(read_only_model)]
assert len(store["untagged_sink"]) == 0, \
"The IDs of the following sink reactions are not tagged with 'SK_'" \
" {}".format(", ".join(store["untagged_demand"]))
[docs]def test_false_sink_reaction(read_only_model, store):
"""Expect all rxns that are tagged with ``SK_`` to be true sink rxns."""
store["false_sink"] = [
rxn.id for rxn in syntax.find_false_sink_rxns(read_only_model)]
assert len(store["false_sink"]) == 0, \
"The IDs of the following reactions are falsely tagged with 'SK_'" \
" {}".format(", ".join(store["false_sink"]))
[docs]def test_exchange_reaction_tag_match(read_only_model, store):
"""Expect all exchange reaction IDs to be prefixed with ``EX_``."""
store["untagged_exchange"] = [
rxn.id for rxn in syntax.find_untagged_exchange_rxns(read_only_model)]
assert len(store["untagged_exchange"]) == 0, \
"The IDs of the following demand reactions are not tagged with 'EX_'" \
" {}".format(", ".join(store["untagged_exchange"]))
[docs]def test_false_exchange_reaction(read_only_model, store):
"""Expect all rxns that are tagged with ``EX_`` to be true exchange rxns."""
store["false_exchange"] = [
rxn.id for rxn in syntax.find_false_exchange_rxns(read_only_model)]
assert len(store["false_exchange"]) == 0, \
"The IDs of the following reactions are falsely tagged with 'EX_'" \
" {}".format(", ".join(store["false_exchange"]))
