def test_invalid_argument(self):
"""
Test that exceptions can be caught and they have the expected message
"""
tmp = numpy.asarray([
2, 38, 7, 0, 90, 4, 1, 0, -12, -56, 15, 64, -98, 35, 12, 64, 0, 0,
0, 0, 0, 0, 0, 0, 46, 1, 17, 1, 0, 0, 0, 0, 96, -41, -104, 36, 122,
-86, -46, -120, 7, 0, -66, 4, 1, 0, 96, -43, 14, 64, -63, 49, 13,
64, 0, 0, 0, 0, 0, 0, 0, 0, 56, 1, 17, 1, 0, 0, 0, 0, 112, 125, 77,
38, 122, -86, -46, -120, 7, 0, 66, 8, 1, 0, 74, -68, 6, 64, -118,
-7, 8, 64, 0, 0, 0, 0, 0, 0, 0, 0, 93, 1, 46, 1, 0, 0, 0, 0, -47,
-104, 2, 40, 122, -86, -46, -120
],
dtype=numpy.uint8)
run = py_interop_run_metrics.run_metrics()
py_interop_comm.read_interop_from_buffer(tmp,
run.extraction_metric_set())
try:
buf = numpy.zeros(3, dtype=numpy.uint8)
py_interop_comm.write_interop_to_buffer(
run.extraction_metric_set(), buf)
self.fail("invalid_argument should have been thrown")
except py_interop_comm.invalid_argument as ex:
self.assertEqual(str(ex).split('\n')[0], "Buffer size too small")
def test_bad_format_exception(self):
"""
Test that exceptions can be caught and they have the expected message
"""
tmp = numpy.asarray([
0, 3, 7, 0, 90, 4, 1, 0, -12, -56, 15, 64, -98, 35, 12, 64, 0, 0,
0, 0, 0, 0, 0, 0, 46, 1, 17, 1, 0, 0, 0, 0, 96, -41, -104, 36, 122,
-86, -46, -120, 7, 0, -66, 4, 1, 0, 96, -43, 14, 64, -63, 49, 13,
64, 0, 0, 0, 0, 0, 0, 0, 0, 56, 1, 17, 1, 0, 0, 0, 0, 112, 125, 77,
38, 122, -86, -46, -120, 7, 0, 66, 8, 1, 0, 74, -68, 6, 64, -118,
-7, 8, 64, 0, 0, 0, 0, 0, 0, 0, 0, 93, 1, 46, 1, 0, 0, 0, 0, -47,
-104, 2, 40, 122, -86, -46, -120
],
dtype=numpy.uint8)
run = py_interop_run_metrics.run_metrics()
try:
py_interop_comm.read_interop_from_buffer(
tmp, run.extraction_metric_set())
self.fail("bad_format_exception should have been thrown")
except py_interop_comm.bad_format_exception as ex:
self.assertEqual(
str(ex).split('\n')[0],
"No format found to parse ExtractionMetricsOut.bin with version: 0 of 2"
)
def test_incomplete_file_exception(self):
"""
Test that exceptions can be caught and they have the expected message
"""
tmp = numpy.asarray([
3, 38, 7, 0, 90, 4, 1, 0, -12, -56, 15, 64, -98, 35, 12, 64, 0, 0,
0, 0, 0, 0, 0, 0, 46, 1, 17, 1, 0, 0, 0, 0, 96, -41, -104, 36, 122,
-86, -46, -120, 7, 0, -66, 4, 1, 0, 96, -43, 14, 64, -63, 49, 13,
64, 0, 0, 0, 0, 0, 0, 0, 0, 56, 1, 17, 1, 0, 0, 0, 0, 112, 125, 77,
38, 122, -86, -46, -120, 7, 0, 66, 8, 1, 0, 74, -68, 6, 64, -118,
-7, 8, 64, 0, 0, 0, 0, 0, 0, 0, 0, 93, 1, 46, 1, 0, 0, 0, 0, -47,
-104, 2, 40, 122, -86, -46, -120
],
dtype=numpy.uint8)
run = py_interop_run_metrics.run_metrics()
try:
py_interop_comm.read_interop_from_buffer(
tmp, run.extraction_metric_set())
self.fail("incomplete_file_exception should have been thrown")
except py_interop_comm.incomplete_file_exception as ex:
self.assertEqual(
str(ex).split('\n')[0],
"Insufficient data read from the file, got: 13 != expected: 50 for Extraction v3"
)
def test_populate_imaging_table(self):
"""
Test if imaging logic can be properly used
"""
tmp = numpy.asarray([2,38
,7,0,90,4,1,0,-12,-56,15,64,-98,35,12,64,0,0,0,0,0,0,0,0,46,1,17,1,0,0,0,0,96,-41,-104,36,122,-86,-46,-120
,7,0,-66,4,1,0,96,-43,14,64,-63,49,13,64,0,0,0,0,0,0,0,0,56,1,17,1,0,0,0,0,112,125,77,38,122,-86,-46,-120
,7,0,66,8,1,0,74,-68,6,64,-118,-7,8,64,0,0,0,0,0,0,0,0,93,1,46,1,0,0,0,0,-47,-104,2,40,122,-86,-46,-120],
dtype=numpy.uint8)
run = py_interop_run_metrics.run_metrics()
py_interop_comm.read_interop_from_buffer(tmp, run.extraction_metric_set())
self.assertEqual(run.extraction_metric_set().size(), 3)
reads = py_interop_run.read_info_vector()
reads.append(py_interop_run.read_info(1, 1, 26))
reads.append(py_interop_run.read_info(2, 27, 76))
run.run_info(py_interop_run.info(
py_interop_run.flowcell_layout(2, 2, 2, 16),
reads
))
run.legacy_channel_update(py_interop_run.HiSeq)
columns = py_interop_table.imaging_column_vector()
py_interop_table.create_imaging_table_columns(run, columns)
row_offsets = py_interop_table.map_id_offset()
py_interop_table.count_table_rows(run, row_offsets)
column_count = py_interop_table.count_table_columns(columns)
data = numpy.zeros((len(row_offsets), column_count), dtype=numpy.float32)
py_interop_table.populate_imaging_table_data(run, columns, row_offsets, data.ravel())
self.assertEqual(data[0, 0], 7)