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import os.path as osp
import os
from pathlib import Path
from h5py import File
import numpy as np
from pytest import fixture, raises
import pytest
from tempfile import TemporaryDirectory
from extra_data.validation import FileAccess, FileValidator, RunValidator, ValidationError, main
from . import make_examples
@fixture(scope='function')
def agipd_file():
with TemporaryDirectory() as td:
path = osp.join(td, 'RAW-R0239-AGIPD00-S00000.h5')
make_examples.make_agipd_file(path)
yield path
@fixture(scope='function')
def data_aggregator_file():
with TemporaryDirectory() as td:
path = osp.join(td, 'RAW-R0450-DA01-S00001.h5')
make_examples.make_fxe_da_file(path)
yield path
def test_validate_run(mock_fxe_raw_run):
rv = RunValidator(mock_fxe_raw_run)
rv.validate()
@pytest.mark.skipif(os.getuid() == 0, reason="Requires a non-root user")
def test_file_error(mock_fxe_raw_run):
not_readable = Path(mock_fxe_raw_run) / 'notReadable.h5'
not_readable.touch(mode=0o066)
problems = RunValidator(mock_fxe_raw_run).run_checks()
assert len(problems) == 1
assert problems[0]['msg'] == 'Could not access file'
assert problems[0]['file'] == str(not_readable)
def test_zeros_in_train_ids(agipd_file):
with File(agipd_file, 'r+') as f:
# introduce zeros in trainId
f['/INDEX/trainId'][12] = 0
with raises(ValidationError) as excinfo:
FileValidator(FileAccess(agipd_file)).validate()
problem = excinfo.value.problems[0]
assert problem['msg'] == 'Zeroes in trainId index before last train ID'
assert problem['dataset'] == 'INDEX/trainId'
assert 'RAW-R0239-AGIPD00-S00000.h5' in problem['file']
def test_non_strictly_increasing_train_ids(agipd_file):
with File(agipd_file, 'r+') as f:
# introduce non strictly increasing trainId
f['/INDEX/trainId'][10] = 11010
f['/INDEX/trainId'][20] = 5
with raises(ValidationError) as excinfo:
FileValidator(FileAccess(agipd_file)).validate()
problem = excinfo.value.problems.pop()
assert problem['msg'] == 'Train IDs are not strictly increasing, e.g. at 10 (11010 >= 10011)'
assert problem['dataset'] == 'INDEX/trainId'
assert 'RAW-R0239-AGIPD00-S00000.h5' in problem['file']
def test_index_pointing_outside_dataset(data_aggregator_file):
with File(data_aggregator_file, 'r+') as f:
# index pointing outside dataset
f['/INDEX/FXE_XAD_GEC/CAM/CAMERA:daqOutput/data/first'][30] = 999
with raises(ValidationError) as excinfo:
FileValidator(FileAccess(data_aggregator_file)).validate()
assert 'Index referring to data (1000) outside dataset (400)' in str(excinfo.value)
def test_invalid_first_dataset(data_aggregator_file):
with File(data_aggregator_file, 'a') as f:
# invalid first shape
length = len(f['INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data/first'])
f['INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data/first'].resize((length+1,))
with raises(ValidationError) as excinfo:
FileValidator(FileAccess(data_aggregator_file)).validate()
problem = excinfo.value.problems.pop()
assert problem['msg'] == 'Index first & count have different number of entries'
assert problem['dataset'] == 'INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data'
assert problem['first_shape'] == (401,)
assert problem['count_shape'] == (400,)
assert 'RAW-R0450-DA01-S00001.h5' in problem['file']
def test_invalid_first_and_count_dataset(data_aggregator_file):
with File(data_aggregator_file, 'a') as f:
# invalid first/index shape
length = len(f['INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data/first'])
f['INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data/first'].resize((length-1,))
length = len(f['INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data/count'])
f['INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data/count'].resize((length-1,))
with raises(ValidationError) as excinfo:
FileValidator(FileAccess(data_aggregator_file)).validate()
problem = excinfo.value.problems.pop()
assert problem['msg'] == 'Index has wrong number of entries'
assert problem['dataset'] == 'INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data'
assert problem['index_shape'] == (399,)
assert problem['trainids_shape'] == (400,)
assert 'RAW-R0450-DA01-S00001.h5' in problem['file']
def test_first_dataset_not_starting_from_zero(data_aggregator_file):
with File(data_aggregator_file, 'a') as f:
# first index not starting at zero
f['INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data/first'][0] = 1
with raises(ValidationError) as excinfo:
FileValidator(FileAccess(data_aggregator_file)).validate()
assert "Index doesn't start at 0" in str(excinfo.value)
assert "INDEX/SA1_XTD2_XGM/DOOCS/MAIN:output/data" in str(excinfo.value)
def test_overlap(agipd_file):
with File(agipd_file, 'r+') as f:
# overlap first index
f['INDEX/SPB_DET_AGIPD1M-1/DET/0CH0:xtdf/image/first'][1] = 0
f['INDEX/SPB_DET_AGIPD1M-1/DET/0CH0:xtdf/image/count'][1] = 128 # no gaps
with raises(ValidationError) as excinfo:
FileValidator(FileAccess(agipd_file)).validate()
problem = excinfo.value.problems.pop()
assert problem['msg'] == 'Overlaps (1) in index, e.g. at 0 (0 + 64 > 0)'
assert problem['dataset'] == 'INDEX/SPB_DET_AGIPD1M-1/DET/0CH0:xtdf/image'
assert 'RAW-R0239-AGIPD00-S00000.h5' in problem['file']
def test_gaps(agipd_file):
with File(agipd_file, 'r+') as f:
# gap in index
f['INDEX/SPB_DET_AGIPD1M-1/DET/0CH0:xtdf/image/first'][1] = 0
f['INDEX/SPB_DET_AGIPD1M-1/DET/0CH0:xtdf/image/count'][0] = 0
with raises(ValidationError) as excinfo:
FileValidator(FileAccess(agipd_file)).validate()
problem = excinfo.value.problems.pop()
assert problem['msg'] == 'Gaps (1) in index, e.g. at 1 (0 + 64 < 128)'
assert problem['dataset'] == 'INDEX/SPB_DET_AGIPD1M-1/DET/0CH0:xtdf/image'
assert 'RAW-R0239-AGIPD00-S00000.h5' in problem['file']
def test_file_without_data(mock_empty_file):
FileValidator(FileAccess(mock_empty_file)).validate()
def test_control_data_timestamps(data_aggregator_file):
with File(data_aggregator_file, 'r+') as f:
# control data timestamp is not in data
ts = f['CONTROL/SA1_XTD2_XGM/DOOCS/MAIN/pulseEnergy/photonFlux/timestamp']
ts[:] = np.arange(len(ts)) + 1
ts[10] = 5
with raises(ValidationError) as excinfo:
FileValidator(FileAccess(data_aggregator_file)).validate()
problem = excinfo.value.problems.pop()
assert problem['msg'] == 'Timestamp is decreasing, e.g. at 10 (5 < 10)'
assert problem['dataset'] == 'CONTROL/SA1_XTD2_XGM/DOOCS/MAIN/pulseEnergy/photonFlux/timestamp'
assert 'RAW-R0450-DA01-S00001.h5' in problem['file']
def test_main_file_non_h5(tmp_path, capsys):
not_h5 = tmp_path / 'notHDF5.h5'
not_h5.write_text("Accessible file, not HDF5")
status = main([str(not_h5)])
assert status == 1
assert 'Could not open HDF5 file' in capsys.readouterr().out
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