def test_hdf5_response(self):
endpoint = '/run/run'
archive_filename = os.path.join(
self.FIXTURES_DIRNAME,
'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex')
data = MultiDict([
('_type', 'SimulationRun'),
('archiveUrl', 'https://web.site/archive.omex'),
('simulator', 'copasi'),
])
with app.app.app.test_client() as client:
with open(archive_filename, 'rb') as archive_file:
with mock.patch('requests.get',
return_value=mock.Mock(
raise_for_status=lambda: None,
content=archive_file.read())):
response = client.post(
endpoint,
data=data,
content_type="multipart/form-data",
headers={'Accept': 'application/x-hdf'})
self.assertEqual(response.status_code, 200, response.json)
h5_filename = os.path.join(self.tmp_dirname, 'reports.h5')
with open(h5_filename, 'wb') as file:
file.write(response.data)
self.assertEqual([
'BIOMD0000000912_sim.sedml/BIOMD0000000912_report',
'BIOMD0000000912_sim.sedml/plot_1'
],
ReportReader().get_ids(self.tmp_dirname))
archive_dirname = os.path.join(self.tmp_dirname, 'archive')
CombineArchiveReader().run(archive_filename, archive_dirname)
sed_doc = SedmlSimulationReader().run(
os.path.join(archive_dirname, 'BIOMD0000000912_sim.sedml'))
report = next(output for output in sed_doc.outputs
if output.id == 'BIOMD0000000912_report')
data_set_results = ReportReader().run(
report, self.tmp_dirname,
'BIOMD0000000912_sim.sedml/BIOMD0000000912_report')
self.assertEqual(
set(data_set_results.keys()),
set([
'data_set_time',
'data_set_T',
'data_set_E',
'data_set_I',
]),
)
numpy.testing.assert_allclose(data_set_results['data_set_time'],
numpy.linspace(0., 1000., 5001))
for values in data_set_results.values():
self.assertEqual(values.shape, (5001, ))
self.assertFalse(numpy.any(numpy.isnan(values)))
def _assert_combine_archive_outputs(self, doc, out_dir):
self.assertEqual(set(['reports.h5', 'reports.zip', 'sim_1.sedml']).difference(set(os.listdir(out_dir))), set())
report = doc.outputs[0]
# check HDF report
report_results = ReportReader().run(report, out_dir, 'sim_1.sedml/report_1', format=report_data_model.ReportFormat.h5)
self.assertEqual(sorted(report_results.keys()), sorted([d.id for d in doc.outputs[0].data_sets]))
sim = doc.tasks[0].simulation
self.assertEqual(len(report_results[report.data_sets[0].id]), sim.number_of_points + 1)
numpy.testing.assert_allclose(
report_results[report.data_sets[0].id],
numpy.linspace(sim.output_start_time, sim.output_end_time, sim.number_of_points + 1),
)
for data_set_result in report_results.values():
self.assertFalse(numpy.any(numpy.isnan(data_set_result)))
# check CSV report
report_results = ReportReader().run(report, out_dir, 'sim_1.sedml/report_1', format=report_data_model.ReportFormat.csv)
self.assertEqual(sorted(report_results.keys()), sorted([d.id for d in doc.outputs[0].data_sets]))
sim = doc.tasks[0].simulation
self.assertEqual(len(report_results[report.data_sets[0].id]), sim.number_of_points + 1)
numpy.testing.assert_allclose(
report_results[report.data_sets[0].id],
numpy.linspace(sim.output_start_time, sim.output_end_time, sim.number_of_points + 1),
)
for data_set_result in report_results.values():
self.assertFalse(numpy.any(numpy.isnan(data_set_result)))
def _assert_combine_archive_outputs(self, doc, out_dir):
results = ReportReader().run(doc.outputs[0],
out_dir,
os.path.join('sim_1.sedml',
doc.outputs[0].id),
format=ReportFormat.h5)
self.assertEqual(
set(results.keys()),
set(['data_set_time', 'data_set_red', 'data_set_green']))
numpy.testing.assert_allclose(results['data_set_time'],
numpy.linspace(0.1, 0.2, 11))
for result in results.values():
self.assertEqual(result.shape, (11, ))
self.assertFalse(numpy.any(numpy.isnan(result)))
def test_more_complex_archive(self):
archive_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'BIOMD0000000297.edited.omex')
config = get_config()
config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv]
config.VIZ_FORMATS = []
config.BUNDLE_OUTPUTS = True
config.KEEP_INDIVIDUAL_OUTPUTS = True
_, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname, config=config)
if log.exception:
raise log.exception
self.assertEqual(set(['reports.zip', 'reports.h5', 'ex1', 'ex2']).difference(set(os.listdir(self.dirname))), set())
self.assertEqual(set(os.listdir(os.path.join(self.dirname, 'ex1'))), set(['BIOMD0000000297.sedml']))
self.assertEqual(set(os.listdir(os.path.join(self.dirname, 'ex2'))), set(['BIOMD0000000297.sedml']))
self.assertEqual(set(os.listdir(os.path.join(self.dirname, 'ex1', 'BIOMD0000000297.sedml'))),
set(['two_species.csv', 'three_species.csv']))
self.assertEqual(set(os.listdir(os.path.join(self.dirname, 'ex2', 'BIOMD0000000297.sedml'))),
set(['one_species.csv', 'four_species.csv']))
archive = ArchiveReader().run(os.path.join(self.dirname, 'reports.zip'))
self.assertEqual(
sorted(file.archive_path for file in archive.files),
sorted([
'ex1/BIOMD0000000297.sedml/two_species.csv',
'ex1/BIOMD0000000297.sedml/three_species.csv',
'ex2/BIOMD0000000297.sedml/one_species.csv',
'ex2/BIOMD0000000297.sedml/four_species.csv',
]),
)
report = sedml_data_model.Report(
data_sets=[
sedml_data_model.DataSet(id='data_set_time_two_species', label='time'),
sedml_data_model.DataSet(id='data_set_Cln4', label='Cln4'),
sedml_data_model.DataSet(id='data_set_Swe13', label='Swe13'),
]
)
report_results = ReportReader().run(report, self.dirname,
'ex1/BIOMD0000000297.sedml/two_species',
format=report_data_model.ReportFormat.h5)
self.assertEqual(sorted(report_results.keys()), sorted(['data_set_time_two_species', 'data_set_Cln4', 'data_set_Swe13']))
numpy.testing.assert_allclose(report_results['data_set_time_two_species'], numpy.linspace(0., 1., 10 + 1))
def assert_outputs_created(self, dirname):
self.assertTrue(os.path.isfile(os.path.join(dirname, 'reports.h5')))
report = sedml_data_model.Report(data_sets=[
sedml_data_model.DataSet(id='time', label='time'),
])
report_results = ReportReader().run(
report,
dirname,
'simulation_1.sedml/simulation_1',
format=report_data_model.ReportFormat.h5)
self.assertEqual(len(report_results[report.data_sets[0].id]), 100 + 1)
numpy.testing.assert_almost_equal(
report_results[report.data_sets[0].id],
numpy.linspace(0., 100., 100 + 1),
)
for data_set_result in report_results.values():
self.assertFalse(numpy.any(numpy.isnan(data_set_result)))
def _assert_combine_archive_outputs(self, doc, out_dir):
# read the report of the results of the execution of the COMBINE archive
report = doc.outputs[0]
report_results = ReportReader().run(
report,
out_dir,
'simulation_1.sedml/simulation_1',
format=report_data_model.ReportFormat.h5)
# assert that the execution of the archive produced the expected results
expected_report_results = report_data_model.DataSetResults({})
for data_set in report.data_sets:
numpy.testing.assert_almost_equal(
report_results[data_set.id],
expected_report_results[data_set.id])