This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tools.verify.asserts.hdf5

import io

    import h5py
except ImportError:
    h5py = None

IMPORT_MISSING_MESSAGE = "h5 assertion requires unavailable optional dependency h5py"

def _assert_h5py():
    if h5py is None:
        raise Exception(IMPORT_MISSING_MESSAGE)

[docs]def assert_has_h5_attribute(output_bytes, key, value): """Asserts the specified HDF5 output has a given key-value pair as HDF5 attribute""" _assert_h5py() output_temp = io.BytesIO(output_bytes) local_attrs = h5py.File(output_temp, 'r').attrs assert key in local_attrs and str(local_attrs[key]) == value, ( "Not a HDF5 file or H5 attributes do not match:\n\t%s\n\n\t(%s : %s)" % (local_attrs.items(), key, value))
[docs]def assert_has_h5_keys(output_bytes, keys): """ Asserts the specified HDF5 output has exactly the given keys.""" _assert_h5py() keys = [k.strip() for k in keys.strip().split(',')] h5_keys = sorted(keys) output_temp = io.BytesIO(output_bytes) local_keys = sorted(list(h5py.File(output_temp, 'r').keys())) assert local_keys == h5_keys, "Not a HDF5 file or H5 keys do not match:\n\t%s\n\t%s" % (local_keys, h5_keys)