test_database.py 文件源码

def timeseriesdata_constructor_existing_file():
    """Tests the TimeSeriesData class constructor when the file exists. Tests
    that the data are as expected, and that the filled data flag is set."""
    tsd = TimeSeriesData("./tests/data/small.h5")
    assert tsd.filled_data
    #Validate that the time-series matrix data are correct
    dat = np.matrix([[0, 2, 0, 0],
                     [2, 1, 3, 4],
                     [1, 1, 1, 1],
                     [0, 0, 1, 0]])
    assert (dat == tsd.get_sparse_matrix().todense()).all()
    assert (tsd.get_time_points() == [0, 4, 10, 12]).all()
    sequence_ids = np.array([b'9247ec5fd33e99387d41e8fc0d7ee278',
                             b'53f74905f7826fee79dd09b0c12caddf',
                             b'8829fefe91ead511a30df118060b1030',
                             b'7f97b4991342bf629966aeac0708c94f'])
    assert (sequence_ids == tsd.get_array_by_chunks("genes/sequenceids")).all()
    sample_names = np.array([b'72c', b'29', b'qpa', b'15'])
    assert (sample_names == tsd.get_array_by_chunks("samples/names")).all()

# __del__(self)
#Test if HDF5 file closed