def test_design_removals():
with FakeProjectContext() as ctx:
# Design with removal of reactions, metabolites, genes
project = GSMProject(ctx.path)
mdl = project.load_model()
rx = mdl.reactions.get_by_id('TPI')
rx.remove_from_model()
gx = mdl.genes.get_by_id("b3916")
gx.name = 'ffoods'
mx = mdl.metabolites.get_by_id('h2o_c')
mx.remove_from_model()
des = project.save_design(mdl,
'test',
'test',
description='test',
overwrite=True)
des._genes.append(
dict(id='ffooo',
name='',
functional=True,
notes=None,
annotation={}))
des._removed_metabolites.append('ttttesssst')
tp = des.load()
assert rx.id not in tp.reactions
assert mx.id not in tp.metabolites
def test_existing_project():
"""
Force project exists exception to be thrown
"""
with FakeProjectContext() as ctx:
with pytest.raises(ProjectConfigurationError):
project_creator(ctx.path, [])
def test_conditions():
with FakeProjectContext() as fp:
# add some growth conditions
fp.add_fake_conditions()
mdl = fp.project.model
load_medium(mdl, dict())
fp.project.save_conditions(mdl,
"bad",
apply_to=fp.project.config.default_model,
observe_growth=False)
# Shouldn't allow conditions that don't grow without being formally specified
with pytest.raises(Infeasible):
fp.project.save_conditions(
mdl, "very bad", apply_to=fp.project.config.default_model)
assert (len(
fp.project.get_conditions(update=True)['growth_conditions']) == 2)
# run the default test
tester = fp.project.project_tester()
tester.collect_tests()
assert (len(tester.default_tests) == 3)
tester.run_all()
# Test the cli interface
runner = CliRunner()
result = runner.invoke(gsmodutils.cli.test,
['--project_path', fp.path, '--verbose'])
assert result.exit_code == 0
def test_json_tests():
""" Test the execution of json tests"""
with FakeProjectContext() as fp:
# Create a fake json file with tests in it
jtest = dict(
test_1=dict(models=[],
conditions=[],
designs=[],
reaction_fluxes=dict(
BIOMASS_Ec_iAF1260_core_59p81M=[0.72, 0.74]),
required_reactions=["DHQS"],
description='TEST JSON TEST'))
project = GSMProject(fp.path)
tpath = os.path.join(project.tests_dir, 'test_x.json')
# write to project path
with open(tpath, "w+") as ff:
json.dump(jtest, ff)
jtest = dict(
test_1=dict(conditions=[],
designs=[],
reaction_fluxes=dict(
BIOMASS_Ec_iAF1260_core_59p81M=[0.72, 0.74]),
required_reactions=["DHQS"],
description='TEST JSON TEST'))
project = GSMProject(fp.path)
tpath = os.path.join(project.tests_dir, 'test_invalid.json')
# write to project path
with open(tpath, "w+") as ff:
json.dump(jtest, ff)
tpath = os.path.join(project.tests_dir, 'test_load_error.json')
with open(tpath, 'w+') as tt:
tt.write('not json\n')
# run test functions
tester = project.project_tester()
tester.collect_tests()
assert len(tester.json_tests) == 1
tester.run_all()
assert len(tester.load_errors) == 1
assert len(tester.invalid_tests) == 1
runner = CliRunner()
result = runner.invoke(gsmodutils.cli.test,
['--project_path', fp.path, '--verbose'])
assert result.exit_code == 0
result = runner.invoke(gsmodutils.cli.test, [
'--project_path', fp.path, '--verbose', '--test_id', 'test_x.json'
])
assert result.exit_code == 0
def test_existing_conditions_file():
"""
Test a project where there is no project file but an existing growth conditions configuration
"""
with FakeProjectContext() as ctx:
os.remove(os.path.join(ctx.path, default_project_file))
with pytest.raises(ProjectConfigurationError):
project_creator(ctx.path, [])
def test_save_infeasible_design():
with FakeProjectContext() as fp:
model = fp.project.model
with pytest.raises(Infeasible):
for m in model.medium:
model.reactions.get_by_id(m).lower_bound = 0
fp.project.save_design(model, 'foo', 'test')
def test_load_conditions():
with FakeProjectContext() as ctx:
project = GSMProject(ctx.path)
model = project.model
# Growth on xylose instead of glucose
model.reactions.EX_xyl__D_e.lower_bound = -8.00
model.reactions.EX_glc__D_e.lower_bound = 0.0
model.reactions.EX_h_e.objective_coefficient = 1.0
project.save_conditions(model,
'xylose_growth',
carbon_source="EX_xyl__D_e")
# The model should be reloaded so it isn't the same reference
del model
new_model = project.load_conditions('xylose_growth')
assert new_model.reactions.EX_xyl__D_e.lower_bound == -8.00
assert new_model.reactions.EX_xyl__D_e.upper_bound == -8.00
assert new_model.reactions.EX_glc__D_e.lower_bound == 0.0
# Test model objective
assert new_model.reactions.EX_h_e.objective_coefficient == 1.0
assert new_model.reactions.BIOMASS_Ec_iAF1260_core_59p81M.objective_coefficient == 1.0
del new_model
model = project.model
# test using a copy of the model
too_model = project.load_conditions('xylose_growth',
model=model,
copy=True)
model.reactions.EX_xyl__D_e.lower_bound = 0.00
assert model.reactions.EX_xyl__D_e.lower_bound != too_model.reactions.EX_xyl__D_e.lower_bound
# Model growth when it shouldn't
with pytest.raises(AssertionError):
project.save_conditions(too_model,
'xylose_growth2',
carbon_source="EX_xyl__D_e",
observe_growth=False)
# Bad "apply_to" model
with pytest.raises(KeyError):
project.save_conditions(too_model,
'xylose_growth3',
carbon_source="EX_xyl__D_e",
apply_to=["FOO"])
# Bad growth target
with pytest.raises(KeyError):
project.save_conditions(too_model,
'xylose_growth3',
carbon_source="EX_foo")
def test_stoich_st():
convert_stoich({"a": -1, "b": -1, "c": 1})
with pytest.raises(TypeError):
equal_stoich({}, {})
with FakeProjectContext() as ctx:
model = ctx.project.model
assert equal_stoich(model.reactions[20], model.reactions[20])
assert not equal_stoich(model.reactions[20], model.reactions[30])
def test_biomass_debug():
with pytest.raises(TypeError):
biomass_debug(None, 'foo')
with FakeProjectContext() as ctx:
# Valid model
model = ctx.project.model
# Remove way of producing
non_products = biomass_debug(
model, model.reactions.BIOMASS_Ec_iAF1260_core_59p81M)
assert len(non_products) == 0
def test_project_update():
with FakeProjectContext() as ctx:
project = GSMProject(ctx.path)
assert len(project.models)
project.update()
with pytest.raises(ProjectNotFound):
project._project_path = 'NOT_REAL_PATH'
project.update()
# Test non existent designs
with pytest.raises(DesignNotFoundError):
project.get_design("fooooo")
def test_info():
with FakeProjectContext() as ctx:
ctx.add_fake_designs()
ctx.add_fake_conditions()
runner = CliRunner()
result = runner.invoke(gsmodutils.cli.info,
['--project_path', ctx.path])
assert result.exit_code == 0
# Test bad project path fail
result = runner.invoke(gsmodutils.cli.info, [])
assert result.exit_code == -1
# Pointless test for code coverage
runner.invoke(gsmodutils.cli.cli)
def test_save_design():
with FakeProjectContext() as ctx:
ctx.add_fake_conditions()
ctx.add_fake_designs()
project = GSMProject(ctx.path)
design = project.get_design("mevalonate_cbb")
mdl = GSModutilsModel(project, design=design)
mdl.save_model()
# Can't save py designs that have been modified
with pytest.raises(NotImplementedError):
design = project.get_design("fake_testpy")
mdl = GSModutilsModel(project, design=design)
mdl.save_model()
def test_copy():
with FakeProjectContext() as ctx:
project = GSMProject(ctx.path)
assert project.project_path == ctx.path
model = GSModutilsModel(project)
copied = model.copy()
assert model is not copied
for met in copied.metabolites:
assert met is not model.metabolites.get_by_id(met.id)
assert met.model is not model
for gene in copied.genes:
assert gene is not model.genes.get_by_id(gene.id)
assert gene.model is not model
def test_addmodel():
with FakeProjectContext() as ctx:
runner = CliRunner()
result = runner.invoke(gsmodutils.cli.addmodel,
[_CORE_MODEL_PATH, '--project_path', ctx.path])
assert result.exit_code == 0
project = GSMProject(ctx.path)
assert "e_coli_core.json" in project.config.models
# Should fail when model already exists
result = runner.invoke(gsmodutils.cli.addmodel,
[_CORE_MODEL_PATH, '--project_path', ctx.path])
assert result.exit_code == -1
def test_create_project():
"""
Create a test project with an example e coli model
"""
# When writing tests use a different folder for multiprocess!
with FakeProjectContext() as ctx:
# Make sure all files exist
assert os.path.exists(ctx.path)
assert os.path.exists(os.path.join(ctx.path, default_project_file))
assert os.path.exists(
os.path.join(ctx.path, default_model_conditionsfp))
# check project loads
GSMProject(ctx.path)
def test_existing_dir():
"""
Tests existing directory and folder
assumes test_create_project works
"""
with FakeProjectContext() as ctx:
# create an existing project and delete the config files
os.remove(os.path.join(ctx.path, default_project_file))
os.remove(os.path.join(ctx.path, default_model_conditionsfp))
project_creator(ctx.path, [])
assert os.path.exists(os.path.join(ctx.path, default_project_file))
assert os.path.exists(
os.path.join(ctx.path, default_model_conditionsfp))
def test_model_tests():
code_str = """
# Look our tests are python 2 compatible!
# p.s. if you're reading this you're such a nerd
from __future__ import print_function
from gsmodutils.test.utils import ModelTestSelector
@ModelTestSelector(designs=["mevalonate_cbb"])
def test_funcdes(model, project, log):
log.assertion(False, "Works", "Does not work", "Test1")
@ModelTestSelector(conditions=["xyl_src"])
def test_func(model, project, log):
log.assertion(True, "Works", "Does not work", "Test2")
"""
with FakeProjectContext(use_second_model=True) as ctx:
ctx.add_fake_conditions()
ctx.add_fake_designs()
test_codep = 'test_code.py'
tfp = os.path.join(ctx.project.tests_dir, test_codep)
with open(tfp, "w+") as codef:
codef.write(code_str)
# Test a design
design = ctx.project.load_design("mevalonate_cbb")
testsdes = design.run_tests()
assert len(testsdes) == 2
assert not testsdes[
"test_code.py::test_funcdes::iAF1260.json::mevalonate_cbb"].log.is_success
# Test a model
model = ctx.project.load_model()
tests = model.run_tests()
assert len(tests) == 3
assert tests["model::iAF1260.json"].log.is_success
assert tests["model::iAF1260.json::conditions::xyl_src"].log.is_success
assert tests[
"test_code.py::test_func::iAF1260.json::xyl_src"].log.is_success
# Test a second model
model2 = ctx.project.load_model('e_coli_core.json')
tests2 = model2.run_tests(display_progress=False)
assert len(tests2) == 1
assert tests2["model::e_coli_core.json"].log.is_success
def test_old_conditions():
"""
Test to see if old conditions (without setting objective function) breaks
:return:
"""
with FakeProjectContext() as ctx:
project = GSMProject(ctx.path)
model = project.model
model.reactions.EX_xyl__D_e.lower_bound = -8.00
model.reactions.EX_glc__D_e.lower_bound = 0.0
project.save_conditions(model,
'xylose_growth',
carbon_source="EX_xyl__D_e")
with open(os.path.join(ctx.path,
"model_conditions.json")) as cond_path:
ddict = json.load(cond_path)
del ddict["growth_conditions"]["xylose_growth"]["objective_reactions"]
with open(os.path.join(ctx.path, "model_conditions.json"),
"w") as cond_path:
json.dump(ddict, cond_path)
too_model = project.load_conditions('xylose_growth',
model=model,
copy=True)
model.reactions.EX_xyl__D_e.lower_bound = 0.00
assert model.reactions.EX_xyl__D_e.lower_bound != too_model.reactions.EX_xyl__D_e.lower_bound
# Test bad objective handling
ddict["growth_conditions"]["xylose_growth"]["objective_reactions"] = [
"NOT_REAL"
]
with open(os.path.join(ctx.path, "model_conditions.json"),
"w") as cond_path:
json.dump(ddict, cond_path)
too_model = project.load_conditions('xylose_growth',
model=model,
copy=True)
assert too_model.reactions.BIOMASS_Ec_iAF1260_core_59p81M.objective_coefficient
def test_load_model():
""" Force exceptions to be thrown """
with pytest.raises(IOError):
load_model('/this/path/does/not/exist')
with pytest.raises(TypeError):
# Create a fake file, format is not valid
with tempfile.NamedTemporaryFile() as fp:
load_model(fp.name, file_format="foo")
with FakeProjectContext() as ctx:
model = ctx.project.model
load_medium(model, {}, copy=True)
with pytest.raises(TypeError):
load_medium(model, set())
with pytest.raises(TypeError):
load_medium(set(), dict())
def test_validator():
""" Check models validate properly """
with FakeProjectContext() as ctx:
# Valid model
model = ctx.project.model
result = validate_model(model)
assert len(result['errors']) == 0
# Model that can't grow
for re in model.exchanges:
re.lower_bound = 0
result = validate_model(model)
assert len(result['errors']) == 1
# model without constraints
model = cobra.Model()
result = validate_model(model)
# Should issue warning, this assertion makes sure
assert len(result['warnings']) == 1
def test_db():
with FakeProjectContext() as ctx:
cache_location = os.path.join(ctx.path, '.gsmod_metacyc_db.json')
db = metacyc.parse_db(METACYC_DB_PATH)
db = metacyc.parse_db(METACYC_DB_PATH)
_ = metacyc.build_universal_model(METACYC_DB_PATH,
use_cache=True,
cache_location=cache_location)
_ = metacyc.build_universal_model(METACYC_DB_PATH,
use_cache=True,
cache_location=cache_location)
_ = metacyc.build_universal_model(METACYC_DB_PATH, use_cache=False)
model = ctx.model
metacyc.add_pathway(model,
reaction_ids=["ALCOHOL-DEHYDROG-RXN"],
db_path=METACYC_DB_PATH)
model = ctx.model
metacyc.add_pathway(model,
enzyme_ids=["EC-1.1.1.1"],
db_path=METACYC_DB_PATH)
def test_add_essential_pathways():
"""
Test adding of json test utility
reactions, description = '', reaction_fluxes = None,
models = None, designs = None, conditions = None, overwrite = False
"""
with FakeProjectContext() as fp:
reactions = ['PYK']
# Test bad id
with pytest.raises(TypeError):
fp.project.add_essential_pathway(1, reactions=reactions)
with pytest.raises(TypeError):
fp.project.add_essential_pathway("foo",
reactions=reactions,
models="String")
# Should work without exception
fp.project.add_essential_pathway("foo", reactions=reactions)
# Can't add the same design twice
with pytest.raises(IOError):
fp.project.add_essential_pathway("foo", reactions=reactions)
with pytest.raises(KeyError):
fp.project.add_essential_pathway("foo2",
reactions=reactions,
designs=["foo"])
with pytest.raises(KeyError):
fp.project.add_essential_pathway("foo3",
reactions=reactions,
conditions=["foo"])
with pytest.raises(KeyError):
fp.project.add_essential_pathway("foo4",
reactions=reactions,
models=["foo"])
def test_addmodel_validation():
# Test adding a model that fails validation
with FakeProjectContext() as ctx:
runner = CliRunner()
# Create a fake model which can't grow
npath = os.path.join(ctx.path, 'tmodel.xml')
model = load_model(_CORE_MODEL_PATH)
for media in model.medium:
reaction = model.reactions.get_by_id(media)
reaction.lower_bound = 0
reaction.upper_bound = 0
cobra.io.write_sbml_model(model, npath)
# Try adding it to the project, it should fail with validation on
result = runner.invoke(gsmodutils.cli.addmodel,
[npath, '--project_path', ctx.path])
assert result.exit_code == -1
# Pass with validation off
result = runner.invoke(
gsmodutils.cli.addmodel,
[npath, '--project_path', ctx.path, '--no-validate'])
assert result.exit_code == 0
def test_import_conditions():
with FakeProjectContext() as ctx:
runner = CliRunner()
project = GSMProject(ctx.path)
model = project.load_model()
model.reactions.EX_xyl__D_e.lower_bound = -8.00
model.reactions.EX_glc__D_e.lower_bound = 0.0
save_path = os.path.join(ctx.path, 'tp.json')
cobra.io.save_json_model(model, save_path)
cid = 'xylose_growth'
result = runner.invoke(gsmodutils.cli.iconditions,
[save_path, cid, '--project_path', ctx.path])
assert result.exit_code == 0
# Check we can actually load these conditions
mdl = project.load_conditions(cid)
assert mdl.reactions.EX_xyl__D_e.lower_bound == -8.0
assert mdl.reactions.EX_glc__D_e.lower_bound == 0.0
def test_load_model():
"""
Most of this is for code coverage
:return:
"""
with FakeProjectContext() as ctx:
ctx.add_fake_conditions()
ctx.add_fake_designs()
project = GSMProject(ctx.path)
assert project.project_path == ctx.path
model = GSModutilsModel(project)
assert isinstance(model, cobra.Model)
model.load_conditions("xyl_src")
model.diff()
model.diff(model)
with pytest.raises(TypeError):
model.diff("should break")
# Test loading non design fails
with pytest.raises(TypeError):
GSModutilsModel(project, design={})
with pytest.raises(TypeError):
GSModutilsModel({})
with pytest.raises(IOError):
GSModutilsModel(project, mpath="/this/is/a/fake/path")
model.save_model()
cpy = model.to_cobra_model()
assert not isinstance(cpy, GSModutilsModel)
def test_load_scrumpy():
with FakeProjectContext() as ctx:
project = GSMProject(ctx.path)
assert project.project_path == ctx.path
model = GSModutilsModel(project)
scrumpy_string = """
External(PROTON_i, "WATER")
NADH_DH_ubi:
"NADH" + "UBIQUINONE-8" + 4 PROTON_i -> "UBIQUINOL-8" + 3 PROTON_p + "NAD"
~
NADH_DH_meno:
"NADH" + "Menaquinones" + 4 PROTON_i -> "Menaquinols" + 3 PROTON_p + "NAD"
~
Cytochrome_c_oxidase:
1/2 "OXYGEN-MOLECULE" + "UBIQUINOL-8" + 2 PROTON_i -> "UBIQUINONE-8" + "WATER" + 2 PROTON_p
~
ATPSynth:
"ADP" + "Pi" + 4 PROTON_p -> "ATP" + "WATER" + 3 PROTON_i
~
ATPase:
"ATP" -> "ADP" + "Pi" + x_ATPWork
~
"""
model.add_scrumpy_reactions(scrumpy_string)
assert "NADH_DH_ubi" in model.reactions
assert "NADH_DH_meno" in model.reactions
assert "Cytochrome_c_oxidase" in model.reactions
assert "ATPSynth" in model.reactions
assert "ATPase" in model.reactions
def test_essential_pathways():
"""
Test adding of json test utility
reactions, description = '', reaction_fluxes = None,
models = None, designs = None, conditions = None, overwrite = False
"""
with FakeProjectContext() as fp:
fp.add_fake_conditions()
fp.add_fake_designs()
reactions = ['PYK']
# Test a model
fp.project.add_essential_pathway('model_test', reactions=reactions)
with pytest.raises(IOError):
fp.project.add_essential_pathway('model_test', reactions=reactions)
# Add an essential pathway test for a design only
fp.project.add_essential_pathway('design_test',
reactions=reactions,
designs=['mevalonate_cbb'])
# Test conditions
fp.project.add_essential_pathway('conditions_test',
reactions=reactions,
conditions=['xyl_src'])
assert os.path.exists(
os.path.join(fp.project.tests_dir, 'test_model_test.json'))
assert os.path.exists(
os.path.join(fp.project.tests_dir, 'test_design_test.json'))
assert os.path.exists(
os.path.join(fp.project.tests_dir, 'test_conditions_test.json'))
# Test conditions designs and
tester = fp.project.project_tester()
tester.run_all()
def test_model_loader():
""" Model loader utility tests """
with FakeProjectContext(use_second_model=True) as ctx:
ml = ModelLoader(ctx.project, "e_coli_core.json", None, None)
ctx.add_fake_conditions()
log = ResultRecord("TL")
model = ml.load(log)
assert os.path.basename(model.mpath) == "e_coli_core.json"
assert model.design is None
ctx.add_fake_designs()
ml = ModelLoader(ctx.project, None, "xyl_src", "mevalonate_cbb")
log = ResultRecord("TL2")
model = ml.load(log)
treac = model.reactions.get_by_id("EX_xyl__D_e")
assert isinstance(model.design, StrainDesign)
assert model.design.id == "mevalonate_cbb"
assert treac.lower_bound == -8.0
ml = ModelLoader(ctx.project, None, "xyl_src", None)
log = ResultRecord("TL2")
model = ml.load(log)
treac = model.reactions.get_by_id("EX_xyl__D_e")
assert treac.lower_bound == -8.0
def test_docker():
with FakeProjectContext() as ctx:
# Add some conditions and a design with a parent
project = GSMProject(ctx.path)
model = project.load_model()
model.reactions.EX_xyl__D_e.lower_bound = -8.00
model.reactions.EX_glc__D_e.lower_bound = 0.0
project.save_conditions(model, 'xylose_growth')
nr = model.reactions.EX_glc__D_e.copy()
model.remove_reactions(["EX_glc__D_e"])
project.save_design(model, 'tt1', 'tt1')
model.add_reactions([nr])
project.save_design(model, 'tt2', 'tt2', parent='tt1')
runner = CliRunner()
result = runner.invoke(gsmodutils.cli.docker,
['--project_path', ctx.path])
assert result.exit_code == 0
result = runner.invoke(gsmodutils.cli.docker,
['--project_path', ctx.path, '--overwrite'])
assert result.exit_code == 0
def test_py_design():
""" Tests a working py_design """
py_design = """
from gsmodutils.utils import design_annotation
@design_annotation(name="tester")
def gsmdesign_tester(model, project):
'''This is the description'''
reaction = model.reactions.get_by_id("ATPM")
reaction.bounds = (-999, 999)
return model
@design_annotation()
def gsmdesign_no_return(model, project):
pass
@design_annotation()
def gsmdesign_bad_prototype(model):
return model
@design_annotation(conditions="xylose_growth", description="overridden description")
def gsmdesign_uses_conditions(model, project):
'''orginal description'''
return model
@design_annotation(base_model="e_coli_core.json")
def gsmdesign_uses_base_model(model, project):
return model
@design_annotation(base_model="e_coli_core")
def gsmdesign_bad_base_model(model, project):
return model
"""
broken_file = """
THIS IS CLEARLY BROKEN PYTHON SYNTAX
"""
with FakeProjectContext(use_second_model=True) as ctx:
project = GSMProject(ctx.path)
ndpath = os.path.join(project.design_path, 'design_t1.py')
# Write the design
with open(ndpath, 'w+') as desf:
desf.write(py_design)
# The file is broken but but the project should still load
ndpath = os.path.join(project.design_path, 'design_broken.py')
with open(ndpath, 'w+') as desb:
desb.write(broken_file)
# Should load without error
design = project.get_design("t1_tester")
assert design.is_pydesign
assert design.name == "tester"
assert design.parent is None
assert design.description == "This is the description"
mdl = design.load()
# Check that the code has executed
reaction = mdl.reactions.get_by_id("ATPM")
assert reaction.lower_bound == -999
assert reaction.upper_bound == 999
model = project.model
# Growth on xylose instead of glucose
model.reactions.EX_xyl__D_e.lower_bound = -8.00
model.reactions.EX_glc__D_e.lower_bound = 0.0
project.save_conditions(model, 'xylose_growth', carbon_source="EX_xyl__D_e")
design = project.get_design("t1_uses_conditions")
assert design.description == "overridden description"
assert design.conditions == "xylose_growth"
mdl = design.load()
assert mdl.reactions.EX_glc__D_e.lower_bound == 0
assert mdl.reactions.EX_xyl__D_e.lower_bound == -8.00
with pytest.raises(DesignError):
project.get_design("t1_no_return")
with pytest.raises(DesignError):
project.get_design("t1_bad_prototype")
design = project.get_design("t1_uses_base_model")
assert design.base_model == "e_coli_core.json"
assert len(design.load().reactions) == 95 # Make sure the base model is loaded
with pytest.raises(DesignError):
project.get_design("t1_bad_base_model")
