def test_read_write_error_handling(self):
report_1 = Report(
id='report_1',
data_sets=[
DataSet(id='x', label='X'),
DataSet(id='y', label='Y'),
DataSet(id='z', label='Z'),
],
)
data_set_results_1 = data_model.DataSetResults({
'x':
numpy.array([1., 2.]),
'y':
numpy.array([3., 4.]),
'z':
numpy.array([5., 6.]),
})
rel_path_1 = os.path.join('a/b/c.sedml', report_1.id)
io.ReportWriter().run(report_1,
data_set_results_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.h5)
report_1.data_sets.append(DataSet(id='w', label='W'))
with self.assertWarns(MissingDataWarning):
io.ReportReader().run(report_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.h5)
report_1.data_sets.pop()
report_1.data_sets.pop()
with self.assertWarns(ExtraDataWarning):
io.ReportReader().run(report_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.h5)
data_set_results_1['x'] = numpy.array([1., 2.],
dtype=numpy.dtype('object'))
with self.assertRaisesRegex(TypeError, 'NumPy dtype should be '):
io.ReportWriter().run(report_1,
data_set_results_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.h5)
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])
def test_write_error_handling(self):
with self.assertRaisesRegex(NotImplementedError, 'is not supported'):
io.ReportWriter().run(Report(), None, None, 'a', format='TSV')
report = Report(data_sets=[DataSet(id='x', label='x')])
data_set_results = data_model.DataSetResults({'x': numpy.zeros((3, ))})
io.ReportWriter().run(report,
data_set_results,
self.dirname,
'.',
format=data_model.ReportFormat.csv)
data_set_results['x'] = data_set_results['x'].reshape((3, 1))
with self.assertWarnsRegex(
CannotExportMultidimensionalTableWarning,
'Multidimensional reports cannot be exported'):
io.ReportWriter().run(report,
data_set_results,
self.dirname,
'.',
format=data_model.ReportFormat.csv)
def test_get_ids(self):
report = Report(data_sets=[
DataSet(id='A', label='A'),
DataSet(id='B', label='A'),
], )
results = data_model.DataSetResults({
report.data_sets[0].id:
numpy.array([1, 2, 3]),
report.data_sets[1].id:
numpy.array([4, 5, 6]),
})
for format in [
data_model.ReportFormat.h5, data_model.ReportFormat.csv
]:
filename = os.path.join(self.dirname, 'test')
io.ReportWriter().run(report,
results,
filename,
'a/b/c.sedml/report1',
format=format)
io.ReportWriter().run(report,
results,
filename,
'a/b/c.sedml/report2',
format=format)
io.ReportWriter().run(report,
results,
filename,
'a/b/c.sedml/report3',
format=format)
io.ReportWriter().run(report,
results,
filename,
'a/b/d.sedml/report4',
format=format)
io.ReportWriter().run(report,
results,
filename,
'a/b/report5',
format=format)
io.ReportWriter().run(report,
results,
filename,
'a/b/report6',
format=format)
self.assertEqual(
set(io.ReportReader().get_ids(filename, format=format)),
set([
'a/b/c.sedml/report1',
'a/b/c.sedml/report2',
'a/b/c.sedml/report3',
'a/b/d.sedml/report4',
'a/b/report5',
'a/b/report6',
]))
with self.assertRaisesRegex(NotImplementedError, 'is not supported'):
io.ReportReader().get_ids(filename, format=None)
def test_overwrite_report(self):
report_1 = Report(
id='report_1',
data_sets=[
DataSet(id='x', label='X'),
DataSet(id='y', label='Y'),
DataSet(id='z', label='Z'),
],
)
data_set_results_1 = data_model.DataSetResults({
'x':
numpy.array([1., 2.]),
'y':
numpy.array([3., 4.]),
'z':
numpy.array([5., 6.]),
})
rel_path_1 = os.path.join('a/b/c.sedml', report_1.id)
io.ReportWriter().run(report_1,
data_set_results_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.h5)
data_set_results_2 = io.ReportReader().run(
report_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.h5)
numpy.testing.assert_allclose(data_set_results_2['x'],
numpy.array([1., 2.]))
numpy.testing.assert_allclose(data_set_results_2['y'],
numpy.array([3., 4.]))
numpy.testing.assert_allclose(data_set_results_2['z'],
numpy.array([5., 6.]))
data_set_results_1 = data_model.DataSetResults({
'x':
numpy.array([1., 2.]) + 1.,
'y':
numpy.array([3., 4.]) + 1.,
'z':
numpy.array([5., 6.]) + 1.,
})
io.ReportWriter().run(report_1,
data_set_results_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.h5)
data_set_results_2 = io.ReportReader().run(
report_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.h5)
numpy.testing.assert_allclose(data_set_results_2['x'],
numpy.array([1., 2.]) + 1.)
numpy.testing.assert_allclose(data_set_results_2['y'],
numpy.array([3., 4.]) + 1.)
numpy.testing.assert_allclose(data_set_results_2['z'],
numpy.array([5., 6.]) + 1.)
def test_read_write_duplicate_labels(self):
# labels in same order
report_1 = Report(
id='report_1',
data_sets=[
DataSet(id='x', label='A'),
DataSet(id='y', label='A'),
DataSet(id='z', label='A'),
],
)
data_set_results_1 = data_model.DataSetResults({
'x':
numpy.array([1., 2.]),
'y':
numpy.array([3., 4.]),
'z':
numpy.array([5., 6.]),
})
rel_path_1 = os.path.join('a/b/c.sedml', report_1.id)
io.ReportWriter().run(report_1,
data_set_results_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.csv)
data_set_results_2 = io.ReportReader().run(
report_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.csv)
numpy.testing.assert_allclose(data_set_results_2['x'],
numpy.array([1., 2.]))
numpy.testing.assert_allclose(data_set_results_2['y'],
numpy.array([3., 4.]))
numpy.testing.assert_allclose(data_set_results_2['z'],
numpy.array([5., 6.]))
# labels in different order
report_1 = Report(
id='report_1',
data_sets=[
DataSet(id='x', label='X'),
DataSet(id='y', label='X'),
DataSet(id='z', label='Z'),
],
)
data_set_results_1 = data_model.DataSetResults({
'x':
numpy.array([1., 2.]),
'y':
numpy.array([3., 4.]),
'z':
numpy.array([5., 6.]),
})
rel_path_1 = os.path.join('a/b/c.sedml', report_1.id)
io.ReportWriter().run(report_1,
data_set_results_1,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.csv)
report_2 = Report(
id='report_1',
data_sets=[
DataSet(id='x', label='X'),
DataSet(id='z', label='Z'),
DataSet(id='y', label='X'),
],
)
data_set_results_2 = io.ReportReader().run(
report_2,
self.dirname,
rel_path_1,
format=data_model.ReportFormat.csv)
self.assertEqual(set(data_set_results_2.keys()), set(['z']))
numpy.testing.assert_allclose(data_set_results_2['z'],
numpy.array([5., 6.]))
def test_read_write(self):
report_1 = Report(
id='report_1',
name='report 1',
data_sets=[
DataSet(id='w', label='W'),
DataSet(id='x', label='X'),
DataSet(id='y', label='Y'),
DataSet(id='z', label='Z'),
],
)
report_2 = Report(
id='report_2',
name='report 2',
data_sets=[
DataSet(id='a', label='A'),
DataSet(id='b', label='B'),
DataSet(id='c', label='C'),
DataSet(id='d', label='D'),
],
)
report_3 = Report(
id='report_3',
data_sets=[
DataSet(id='a', label='A'),
DataSet(id='b', label='B'),
DataSet(id='c', label='C'),
DataSet(id='d', label='D'),
],
)
data_set_results_1 = data_model.DataSetResults({
'w':
None,
'x':
numpy.array([1, 2, 3]),
'y':
numpy.array([4., numpy.nan]),
'z':
numpy.array(6.),
})
data_set_results_2 = data_model.DataSetResults({
'a':
numpy.array([1, 2]),
'b':
numpy.array([7., 8., 9.]),
'c':
numpy.array(True),
'd':
None,
})
data_set_results_3 = data_model.DataSetResults({
'a':
numpy.array([[1, 2], [3, 4], [5, 6]]),
'b':
numpy.array([7., 8., 9.]),
'c':
numpy.array(True),
'd':
None,
})
# CSV, TSV
for format in [
data_model.ReportFormat.csv, data_model.ReportFormat.tsv,
data_model.ReportFormat.xlsx
]:
rel_path_1 = os.path.join(format.value, 'a/b/c.sedml', report_1.id)
rel_path_2 = os.path.join(format.value, 'a/d.sedml', report_2.id)
rel_path_3 = os.path.join(format.value, 'e.sedml', report_2.id)
io.ReportWriter().run(report_1,
data_set_results_1,
self.dirname,
rel_path_1,
format=format)
io.ReportWriter().run(report_2,
data_set_results_2,
self.dirname,
rel_path_2,
format=format)
with self.assertWarnsRegex(
CannotExportMultidimensionalTableWarning,
'Multidimensional reports cannot be exported'):
io.ReportWriter().run(report_3,
data_set_results_3,
self.dirname,
rel_path_3,
format=format)
data_set_results_1_b = io.ReportReader().run(report_1,
self.dirname,
rel_path_1,
format=format)
data_set_results_2_b = io.ReportReader().run(report_2,
self.dirname,
rel_path_2,
format=format)
self.assertEqual(
set(io.ReportReader().get_ids(self.dirname, format=format)),
set([rel_path_1, rel_path_2]))
numpy.testing.assert_allclose(
data_set_results_1_b['w'],
numpy.array([numpy.nan, numpy.nan, numpy.nan]))
numpy.testing.assert_allclose(data_set_results_1_b['x'],
numpy.array([1., 2., 3.]))
numpy.testing.assert_allclose(
data_set_results_1_b['y'],
numpy.array([4., numpy.nan, numpy.nan]))
numpy.testing.assert_allclose(
data_set_results_1_b['z'],
numpy.array([6., numpy.nan, numpy.nan]))
self.assertEqual(data_set_results_1_b['w'].dtype.name, 'float64')
self.assertEqual(data_set_results_1_b['x'].dtype.name, 'float64')
self.assertEqual(data_set_results_1_b['y'].dtype.name, 'float64')
self.assertEqual(data_set_results_1_b['z'].dtype.name, 'float64')
numpy.testing.assert_allclose(data_set_results_2_b['a'],
numpy.array([1., 2., numpy.nan]))
numpy.testing.assert_allclose(data_set_results_2_b['b'],
numpy.array([7., 8., 9.]))
numpy.testing.assert_allclose(
data_set_results_2_b['c'],
numpy.array([1., numpy.nan, numpy.nan]))
numpy.testing.assert_allclose(
data_set_results_2_b['d'],
numpy.array([numpy.nan, numpy.nan, numpy.nan]))
self.assertEqual(data_set_results_2_b['a'].dtype.name, 'float64')
self.assertEqual(data_set_results_2_b['b'].dtype.name, 'float64')
self.assertEqual(data_set_results_2_b['c'].dtype.name, 'float64')
self.assertEqual(data_set_results_2_b['d'].dtype.name, 'float64')
# HDF
for format in [data_model.ReportFormat.h5]:
rel_path_1 = os.path.join(format.value, 'a/b/c.sedml', report_1.id)
rel_path_2 = os.path.join(format.value, 'a/d.sedml', report_2.id)
rel_path_3 = os.path.join(format.value, 'e.sedml', report_3.id)
io.ReportWriter().run(report_1,
data_set_results_1,
self.dirname,
rel_path_1,
format=format)
io.ReportWriter().run(report_2,
data_set_results_2,
self.dirname,
rel_path_2,
format=format)
io.ReportWriter().run(report_3,
data_set_results_3,
self.dirname,
rel_path_3,
format=format)
data_set_results_1_b = io.ReportReader().run(report_1,
self.dirname,
rel_path_1,
format=format)
data_set_results_2_b = io.ReportReader().run(report_2,
self.dirname,
rel_path_2,
format=format)
data_set_results_3_b = io.ReportReader().run(report_3,
self.dirname,
rel_path_3,
format=format)
self.assertEqual(
set(io.ReportReader().get_ids(self.dirname, format=format)),
set([rel_path_1, rel_path_2, rel_path_3]))
self.assertEqual(data_set_results_1_b['w'], None)
numpy.testing.assert_allclose(data_set_results_1_b['x'],
numpy.array([1, 2, 3]))
numpy.testing.assert_allclose(data_set_results_1_b['y'],
numpy.array([4., numpy.nan]))
numpy.testing.assert_allclose(data_set_results_1_b['z'],
numpy.array(6.))
self.assertEqual(data_set_results_1_b['x'].dtype.name, 'int64')
self.assertEqual(data_set_results_1_b['y'].dtype.name, 'float64')
self.assertEqual(data_set_results_1_b['z'].dtype.name, 'float64')
numpy.testing.assert_allclose(data_set_results_2_b['a'],
numpy.array([1, 2]))
numpy.testing.assert_allclose(data_set_results_2_b['b'],
numpy.array([7., 8., 9.]))
numpy.testing.assert_allclose(data_set_results_2_b['c'],
numpy.array(True))
self.assertEqual(data_set_results_2_b['d'], None)
self.assertEqual(data_set_results_2_b['a'].dtype.name, 'int64')
self.assertEqual(data_set_results_2_b['b'].dtype.name, 'float64')
self.assertEqual(data_set_results_2_b['c'].dtype.name, 'bool')
numpy.testing.assert_allclose(
data_set_results_3_b['a'], numpy.array([[1, 2], [3, 4], [5,
6]]))
numpy.testing.assert_allclose(data_set_results_3_b['b'],
numpy.array([7., 8., 9.]))
numpy.testing.assert_allclose(data_set_results_3_b['c'],
numpy.array(True))
self.assertEqual(data_set_results_3_b['d'], None)
self.assertEqual(data_set_results_3_b['a'].dtype.name, 'int64')
self.assertEqual(data_set_results_3_b['b'].dtype.name, 'float64')
self.assertEqual(data_set_results_3_b['c'].dtype.name, 'bool')
with h5py.File(os.path.join(self.dirname, 'reports.h5'),
'r') as file:
self.assertEqual(
file[format.value + '/a'].attrs, {
'uri': format.value + '/a',
'combineArchiveLocation': format.value + '/a',
})
self.assertEqual(
file[format.value + '/a/b'].attrs, {
'uri': format.value + '/a/b',
'combineArchiveLocation': format.value + '/a/b',
})
self.assertEqual(
file[format.value + '/a/b/c.sedml'].attrs, {
'uri': format.value + '/a/b/c.sedml',
'combineArchiveLocation':
format.value + '/a/b/c.sedml',
})
self.assertEqual(
file[format.value + '/a/d.sedml'].attrs, {
'uri': format.value + '/a/d.sedml',
'combineArchiveLocation': format.value + '/a/d.sedml',
})
self.assertEqual(
file[format.value + '/e.sedml'].attrs, {
'uri': format.value + '/e.sedml',
'combineArchiveLocation': format.value + '/e.sedml',
})
self.assertEqual(
file[format.value + '/a/b/c.sedml/' +
report_1.id].attrs['uri'],
format.value + '/a/b/c.sedml/' + report_1.id)
self.assertEqual(
file[format.value + '/a/b/c.sedml/' +
report_1.id].attrs['sedmlId'], report_1.id)
self.assertEqual(
file[format.value + '/a/b/c.sedml/' +
report_1.id].attrs['sedmlName'], report_1.name)
self.assertEqual(
file[format.value + '/a/d.sedml/' +
report_2.id].attrs['uri'],
format.value + '/a/d.sedml/' + report_2.id)
self.assertEqual(
file[format.value + '/a/d.sedml/' +
report_2.id].attrs['sedmlId'], report_2.id)
self.assertEqual(
file[format.value + '/a/d.sedml/' +
report_2.id].attrs['sedmlName'], report_2.name)
self.assertEqual(
file[format.value + '/e.sedml/' +
report_3.id].attrs['uri'],
format.value + '/e.sedml/' + report_3.id)
self.assertEqual(
file[format.value + '/e.sedml/' +
report_3.id].attrs['sedmlId'], report_3.id)
self.assertNotIn(
'sedmlName',
file[format.value + '/e.sedml/' + report_3.id].attrs)