def test_test_model_timeout(model):
api.test_model(
model,
solver_timeout=1,
exclusive="test_find_reactions_unbounded_flux_default_condition",
)
assert model.solver.configuration.timeout == 1
def run(model, collect, filename, directory, ignore_git, pytest_args, exclusive,
skip, solver, custom):
"""
Run the test suite and collect results.
MODEL: Path to model file. Can also be supplied via the environment variable
MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'.
"""
if ignore_git:
repo = None
else:
repo = callbacks.probe_git()
if not any(a.startswith("--tb") for a in pytest_args):
pytest_args = ["--tb", "short"] + pytest_args
if not any(a.startswith("-v") for a in pytest_args):
pytest_args.append("-vv")
model.solver = solver
if collect:
if repo is not None and directory is not None:
filename = join(directory,
"{}.json".format(repo.active_branch.commit.hexsha))
code = api.test_model(model, filename, pytest_args=pytest_args,
skip=skip, exclusive=exclusive, custom=custom)
else:
code = api.test_model(model, pytest_args=pytest_args, skip=skip,
exclusive=exclusive, custom=custom)
sys.exit(code)
def history_directory(request, tmpdir_factory):
model = model_builder(request.param)
directory = tmpdir_factory.mkdir("Results")
for i in range(3):
filename = str(directory.join("{}.json".format(i)))
api.test_model(model, filename)
return str(directory)
def test_snapshot_report_file(model, tmpdir):
filename = str(tmpdir.join("index.html"))
_, results = api.test_model(model,
results=True,
pytest_args=["--tb", "no"])
report = api.snapshot_report(results, html=True)
assert report.startswith("<!doctype html>")
def snapshot(model, filename, pytest_args, exclusive, skip, solver,
solver_timeout, experimental, custom_tests, custom_config):
"""
Take a snapshot of a model's state and generate a report.
MODEL: Path to model file. Can also be supplied via the environment variable
MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'.
"""
model_obj, sbml_ver, notifications = api.validate_model(model)
if model_obj is None:
LOGGER.critical(
"The model could not be loaded due to the following SBML errors.")
utils.stdout_notifications(notifications)
api.validation_report(model, notifications, filename)
sys.exit(1)
if not any(a.startswith("--tb") for a in pytest_args):
pytest_args = ["--tb", "no"] + pytest_args
# Add further directories to search for tests.
pytest_args.extend(custom_tests)
config = ReportConfiguration.load()
# Update the default test configuration with custom ones (if any).
for custom in custom_config:
config.merge(ReportConfiguration.load(custom))
model_obj.solver = solver
_, results = api.test_model(model_obj,
sbml_version=sbml_ver,
results=True,
pytest_args=pytest_args,
skip=skip,
exclusive=exclusive,
experimental=experimental,
solver_timeout=solver_timeout)
with open(filename, "w", encoding="utf-8") as file_handle:
LOGGER.info("Writing snapshot report to '%s'.", filename)
file_handle.write(api.snapshot_report(results, config))
def diff(models, filename, pytest_args, exclusive, skip, solver,
experimental, custom_tests, custom_config):
"""
Take a snapshot of all the supplied models and generate a diff report.
MODELS: List of paths to two or more model files.
"""
if not any(a.startswith("--tb") for a in pytest_args):
pytest_args = ["--tb", "no"] + pytest_args
# Add further directories to search for tests.
pytest_args.extend(custom_tests)
config = ReportConfiguration.load()
# Update the default test configuration with custom ones (if any).
for custom in custom_config:
config.merge(ReportConfiguration.load(custom))
# Build the diff report specific data structure
diff_results = dict()
for model_path in models:
try:
model_filename = os.path.basename(model_path)
diff_results.setdefault(model_filename, dict())
model = callbacks._load_model(model_path)
model.solver = solver
_, diff_results[model_filename] = api.test_model(
model, results=True, pytest_args=pytest_args,
skip=skip, exclusive=exclusive, experimental=experimental)
except Exception as e:
LOGGER.warning(
"The following exception occurred while loading model {}: {}"
"".format(model_filename, e))
with open(filename, "w", encoding="utf-8") as file_handle:
LOGGER.info("Writing diff report to '%s'.", filename)
file_handle.write(api.diff_report(diff_results, config))
def run(model, collect, filename, location, ignore_git, pytest_args, exclusive,
skip, solver, experimental, custom_tests, deployment):
"""
Run the test suite on a single model and collect results.
MODEL: Path to model file. Can also be supplied via the environment variable
MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'.
"""
def is_verbose(arg):
return (arg.startswith("--verbosity") or arg.startswith("-v")
or arg.startswith("--verbose") or arg.startswith("-q")
or arg.startswith("--quiet"))
if ignore_git:
repo = None
else:
repo = callbacks.probe_git()
if collect:
if repo is not None:
if location is None:
LOGGER.critical(
"Working with a repository requires a storage location.")
sys.exit(1)
if not any(a.startswith("--tb") for a in pytest_args):
pytest_args = ["--tb", "short"] + pytest_args
if not any(is_verbose(a) for a in pytest_args):
pytest_args.append("-vv")
# Add further directories to search for tests.
pytest_args.extend(custom_tests)
model.solver = solver
code, result = api.test_model(model=model,
results=True,
pytest_args=pytest_args,
skip=skip,
exclusive=exclusive,
experimental=experimental)
if collect:
if repo is None:
manager = ResultManager()
manager.store(result, filename=filename)
else:
LOGGER.info("Checking out deployment branch.")
previous = repo.active_branch
previous_cmt = previous.commit
repo.heads[deployment].checkout()
try:
manager = SQLResultManager(repository=repo, location=location)
except (AttributeError, ArgumentError):
manager = RepoResultManager(repository=repo, location=location)
LOGGER.info(
"Committing result and changing back to working branch.")
manager.store(result, commit=previous_cmt.hexsha)
repo.git.add(".")
repo.index.commit("chore: add result for {}".format(
previous_cmt.hexsha))
previous.checkout()
def _test_history(model, solver, manager, commit, pytest_args, skip, exclusive,
experimental):
model.solver = solver
_, result = api.test_model(model,
results=True,
pytest_args=pytest_args,
skip=skip,
exclusive=exclusive,
experimental=experimental)
manager.store(result, commit=commit)
def _test_history(model, sbml_ver, solver, manager, commit, pytest_args, skip,
exclusive, experimental):
model.solver = solver
# Load the experimental configuration using model information.
if experimental is not None:
experimental.load(model)
_, result = api.test_model(
model, sbml_version=sbml_ver, results=True, pytest_args=pytest_args,
skip=skip, exclusive=exclusive, experimental=experimental)
manager.store(result, commit=commit)
def _test_history(model, sbml_ver, solver, solver_timeout, manager, commit,
pytest_args, skip, exclusive, experimental):
model.solver = solver
# Load the experimental configuration using model information.
if experimental is not None:
experimental.load(model)
_, result = api.test_model(
model, sbml_version=sbml_ver, results=True, pytest_args=pytest_args,
skip=skip, exclusive=exclusive, experimental=experimental,
solver_timeout=solver_timeout)
manager.store(result, commit=commit)
def _test_diff(model_and_model_ver_tuple, pytest_args, skip, exclusive,
experimental, solver_timeout):
model, sbml_ver = model_and_model_ver_tuple
_, diff_results = api.test_model(model,
sbml_version=sbml_ver,
results=True,
pytest_args=pytest_args,
skip=skip,
exclusive=exclusive,
experimental=experimental,
solver_timeout=solver_timeout)
return diff_results
def snapshot(model, filename, pytest_args):
"""
Take a snapshot of a model's state and generate a report.
MODEL: Path to model file. Can also be supplied via the environment variable
MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'.
"""
if not any(a.startswith("--tb") for a in pytest_args):
pytest_args = ["--tb", "short"] + pytest_args
if not any(a.startswith("-v") for a in pytest_args):
pytest_args.append("-vv")
_, results = api.test_model(model, results=True, pytest_args=pytest_args)
api.basic_report(results, filename)
def snapshot(model, filename, pytest_args, solver, custom_tests,
custom_config):
"""
Take a snapshot of a model's state and generate a report.
MODEL: Path to model file. Can also be supplied via the environment variable
MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'.
"""
if not any(a.startswith("--tb") for a in pytest_args):
pytest_args = ["--tb", "no"] + pytest_args
# Add further directories to search for tests.
pytest_args.extend(custom_tests)
config = ReportConfiguration.load()
# Update the default test configuration with custom ones (if any).
for custom in custom_config:
config.merge(ReportConfiguration.load(custom))
model.solver = solver
_, results = api.test_model(model, results=True, pytest_args=pytest_args)
api.snapshot_report(results, config, filename)
def snapshot(model, filename, pytest_args, exclusive, skip, solver,
experimental, custom_tests, custom_config):
"""
Take a snapshot of a model's state and generate a report.
MODEL: Path to model file. Can also be supplied via the environment variable
MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'.
"""
if not any(a.startswith("--tb") for a in pytest_args):
pytest_args = ["--tb", "no"] + pytest_args
# Add further directories to search for tests.
pytest_args.extend(custom_tests)
config = ReportConfiguration.load()
# Update the default test configuration with custom ones (if any).
for custom in custom_config:
config.merge(ReportConfiguration.load(custom))
model.solver = solver
_, results = api.test_model(model, results=True, pytest_args=pytest_args,
skip=skip, exclusive=exclusive,
experimental=experimental)
with open(filename, "w", encoding="utf-8") as file_handle:
LOGGER.info("Writing snapshot report to '%s'.", filename)
file_handle.write(api.snapshot_report(results, config))
def _test_history(model, filename, pytest_args, skip):
model = callbacks.validate_model(None, "model", model)
api.test_model(model, filename, pytest_args=pytest_args, skip=skip)
def test_basic_report_file(model, tmpdir):
filename = str(tmpdir.join("index.html"))
_, results = api.test_model(model, results=True)
api.basic_report(results, filename)
assert exists(filename)
def test_test_model_file(model, tmpdir):
filename = str(tmpdir.join("result.json"))
api.test_model(model, filename)
assert exists(filename)
def test_test_model_result(model):
_, result = api.test_model(model, results=True)
# TODO: Once introduced perform schema checks here.
assert len(result) > 0
def test_test_model_code(model, code):
assert api.test_model(model) == code
def run_memote(self, ctx, params):
"""
:param params: instance of type "RunMemoteParams" -> structure:
parameter "workspace" of String, parameter "model_id" of String,
parameter "media_id" of String, parameter "out_model_id" of String
:returns: instance of type "RunMemoteResults" -> structure: parameter
"model_ref" of String
"""
# ctx is the context object
# return variables are: output
#BEGIN run_memote
print(params)
kbase_api = cobrakbase.KBaseAPI(ctx['token'],
config={'workspace-url': self.ws_url})
modelseed = cobrakbase.modelseed.from_local(
'/kb/module/data/ModelSEEDDatabase')
kmodel_data = kbase_api.get_object(params['model_id'],
params['workspace'])
fbamodel = KBaseFBAModel(kmodel_data)
builder = KBaseFBAModelToCobraBuilder(fbamodel)
if 'genome_ref' in kmodel_data:
logging.info("Annotating model with genome information: %s",
kmodel_data['genome_ref'])
ref_data = kbase_api.get_object_info_from_ref(
kmodel_data['genome_ref'])
genome_data = kbase_api.get_object(ref_data.id,
ref_data.workspace_id)
builder.with_genome(KBaseGenome(genome_data))
media = None
if 'media_id' in params and not params[
'media_id'] == "" and not params['media_id'] == None:
print("MEDIA ID", params['media_id'])
media_data = kbase_api.get_object(params['media_id'],
params['workspace'])
media = KBaseBiochemMedia(media_data)
if media == None:
if 'gapfillings' in kmodel_data and len(
kmodel_data['gapfillings']) > 0:
print("Pulling media from gapfilling...",
kmodel_data['gapfillings'])
ref = kmodel_data['gapfillings'][0]['media_ref']
ref_data = kbase_api.get_object_info_from_ref(ref)
media_data = kbase_api.get_object(ref_data.id,
ref_data.workspace_id)
media = KBaseBiochemMedia(media_data)
if not media == None:
builder.with_media(media)
#converts to cobra model object with builder
model = builder.build()
cobrakbase.annotate_model_with_modelseed(model, modelseed)
#modelseed = cobrakbase.modelseed.from_local('/kb/module/data/ModelSEEDDatabase-dev')
#print(cobrakbase.annotate_model_with_modelseed(model, modelseed))
a, results = memote_api.test_model(model,
results=True,
skip=['test_thermodynamics'])
config = ReportConfiguration.load()
html = memote_api.snapshot_report(results, config)
report_folder = self.shared_folder
with open(report_folder + "/report.html", 'w') as f:
f.write(html)
cobra.io.write_sbml_model(model, report_folder + "/model.xml")
report_client = KBaseReport(self.callback_url)
report_params = {
'direct_html_link_index':
0,
'workspace_name':
params['workspace'],
'report_object_name':
'run_memote_' + uuid.uuid4().hex,
'objects_created': [],
'html_links': [{
'name': 'report',
'description': 'Memote HTML Report',
'path': report_folder + "/report.html"
}],
'file_links': [{
'name': params['model_id'] + ".xml",
'description': 'desc',
'path': report_folder + "/model.xml"
}]
}
report_info = report_client.create_extended_report(report_params)
output = {
'report_name': report_info['name'],
'report_ref': report_info['ref']
}
#END run_memote
# At some point might do deeper type checking...
if not isinstance(output, dict):
raise ValueError('Method run_memote return value ' +
'output is not type dict as required.')
# return the results
return [output]
def run(model, collect, filename, location, ignore_git, pytest_args, exclusive,
skip, solver, experimental, custom_tests, deployment,
skip_unchanged):
"""
Run the test suite on a single model and collect results.
MODEL: Path to model file. Can also be supplied via the environment variable
MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'.
"""
def is_verbose(arg):
return (arg.startswith("--verbosity") or
arg.startswith("-v") or arg.startswith("--verbose") or
arg.startswith("-q") or arg.startswith("--quiet"))
if ignore_git:
repo = None
else:
callbacks.git_installed()
repo = callbacks.probe_git()
if collect:
if repo is not None:
if location is None:
LOGGER.critical(
"Working with a repository requires a storage location.")
sys.exit(1)
if not any(a.startswith("--tb") for a in pytest_args):
pytest_args = ["--tb", "short"] + pytest_args
if not any(is_verbose(a) for a in pytest_args):
pytest_args.append("-vv")
# Check if the model was changed in this commit. Exit `memote run` if this
# was not the case.
if skip_unchanged and repo is not None:
commit = repo.head.commit
if not is_modified(model, commit):
LOGGER.info("The model was not modified in commit '%s'. Skipping.",
commit.hexsha)
sys.exit(0)
# Add further directories to search for tests.
pytest_args.extend(custom_tests)
# Check if the model can be loaded at all.
model, sbml_ver, notifications = api.validate_model(model)
if model is None:
LOGGER.critical(
"The model could not be loaded due to the following SBML errors.")
stdout_notifications(notifications)
sys.exit(1)
model.solver = solver
# Load the experimental configuration using model information.
if experimental is not None:
experimental.load(model)
code, result = api.test_model(
model=model, sbml_version=sbml_ver, results=True,
pytest_args=pytest_args, skip=skip,
exclusive=exclusive, experimental=experimental)
if collect:
if repo is None:
manager = ResultManager()
manager.store(result, filename=filename)
else:
LOGGER.info("Checking out deployment branch.")
# If the repo HEAD is pointing to the most recent branch then
# GitPython's `repo.active_branch` works. Yet, if the repo is in
# detached HEAD state, i.e., when a user has checked out a specific
# commit as opposed to a branch, this won't work and throw a
# `TypeError`, which we are circumventing below.
try:
previous = repo.active_branch
previous_cmt = previous.commit
is_branch = True
except TypeError:
previous_cmt = repo.head.commit
is_branch = False
repo.git.checkout(deployment)
try:
manager = SQLResultManager(repository=repo, location=location)
except (AttributeError, ArgumentError):
manager = RepoResultManager(repository=repo, location=location)
LOGGER.info(
"Committing result and changing back to working branch.")
manager.store(result, commit=previous_cmt.hexsha)
repo.git.add(".")
check_call(
['git', 'commit',
'-m', "chore: add result for {}".format(previous_cmt.hexsha)]
)
if is_branch:
previous.checkout()
else:
repo.commit(previous_cmt)
def run(model, collect, filename, location, ignore_git, pytest_args, exclusive,
skip, solver, solver_timeout, experimental, custom_tests, deployment,
skip_unchanged):
"""
Run the test suite on a single model and collect results.
MODEL: Path to model file. Can also be supplied via the environment variable
MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'.
"""
def is_verbose(arg):
return (arg.startswith("--verbosity") or arg.startswith("-v")
or arg.startswith("--verbose") or arg.startswith("-q")
or arg.startswith("--quiet"))
if ignore_git:
repo = None
else:
callbacks.git_installed()
repo = callbacks.probe_git()
if collect:
if repo is not None:
if location is None:
LOGGER.critical(
"Working with a repository requires a storage location.")
sys.exit(1)
if not any(a.startswith("--tb") for a in pytest_args):
pytest_args = ["--tb", "short"] + pytest_args
if not any(is_verbose(a) for a in pytest_args):
pytest_args.append("-vv")
# Check if the model was changed in this commit. Exit `memote run` if this
# was not the case.
if skip_unchanged and repo is not None:
commit = repo.head.commit
if not is_modified(model, commit):
LOGGER.info("The model was not modified in commit '%s'. Skipping.",
commit.hexsha)
sys.exit(0)
# Add further directories to search for tests.
pytest_args.extend(custom_tests)
# Check if the model can be loaded at all.
model, sbml_ver, notifications = api.validate_model(model)
if model is None:
LOGGER.critical(
"The model could not be loaded due to the following SBML errors.")
stdout_notifications(notifications)
sys.exit(1)
model.solver = solver
code, result = api.test_model(model=model,
sbml_version=sbml_ver,
results=True,
pytest_args=pytest_args,
skip=skip,
exclusive=exclusive,
experimental=experimental,
solver_timeout=solver_timeout)
if collect:
if repo is None:
manager = ResultManager()
manager.store(result, filename=filename)
else:
LOGGER.info("Checking out deployment branch.")
# If the repo HEAD is pointing to the most recent branch then
# GitPython's `repo.active_branch` works. Yet, if the repo is in
# detached HEAD state, i.e., when a user has checked out a specific
# commit as opposed to a branch, this won't work and throw a
# `TypeError`, which we are circumventing below.
try:
previous = repo.active_branch
previous_cmt = previous.commit
is_branch = True
except TypeError:
previous_cmt = repo.head.commit
is_branch = False
repo.git.checkout(deployment)
try:
manager = SQLResultManager(repository=repo, location=location)
except (AttributeError, ArgumentError):
manager = RepoResultManager(repository=repo, location=location)
LOGGER.info(
"Committing result and changing back to working branch.")
manager.store(result, commit=previous_cmt.hexsha)
repo.git.add(".")
repo.git.commit(
"--message",
"chore: add result for {}".format(previous_cmt.hexsha))
if is_branch:
previous.checkout()
else:
repo.commit(previous_cmt)
import json
from memote.suite.api import test_model
import cobra
model = cobra.io.read_sbml_model("WormJam.xml")
code, results = test_model(model, sbml_version=(3, 1),
results=True) # ,skip=["test_consistency"]
with open("results.json", "w+") as f:
f.write(json.dumps(results, indent=4))
print("Memote Done")
